diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml index 4fe2308..d451694 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml @@ -138,3 +138,31 @@ tools: owner: iuc - name: funannotate_sort owner: iuc +- name: staramr + owner: iuc +- name: amrfinderplus + owner: iuc +- name: isescan + owner: iuc +- name: integron_finder + owner: iuc +- name: bakta + owner: iuc +- name: repeatmodeler + owner: csbl +- name: prodigal + owner: iuc +- name: argnorm + owner: iuc +- name: mmseqs2_taxonomy_assignment + owner: iuc +- name: busco + owner: iuc +- name: ncbi_fcs_adaptor + owner: richard-burhans +- name: compleasm + owner: iuc +- name: helixer + owner: genouest +- name: omark + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml.lock index eba16b4..5293a47 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -144,6 +144,7 @@ tools: - name: abricate owner: iuc revisions: + - 3f3e247c053d - c2ef298da409 tool_panel_section_id: annotation tool_panel_section_label: Annotation @@ -162,6 +163,9 @@ tools: - name: column_maker owner: devteam revisions: + - 02026300aa45 + - 427903d47026 + - 6595517c2dd8 - 9cd341095afd - aff5135563c6 tool_panel_section_id: annotation @@ -431,3 +435,91 @@ tools: - d77fdcca400e tool_panel_section_id: annotation tool_panel_section_label: Annotation +- name: staramr + owner: iuc + revisions: + - 6d5c8a6ceea0 + - eaa563bd535a + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: amrfinderplus + owner: iuc + revisions: + - 7844dbe4f8e2 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: isescan + owner: iuc + revisions: + - 81539b9ae80a + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: integron_finder + owner: iuc + revisions: + - bfd290fe1588 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: bakta + owner: iuc + revisions: + - 1942e86e2ee1 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: repeatmodeler + owner: csbl + revisions: + - 4a172d211285 + - 8661b2607b7e + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: prodigal + owner: iuc + revisions: + - 91791b6ecd38 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: argnorm + owner: iuc + revisions: + - d8e95a03321a + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: mmseqs2_taxonomy_assignment + owner: iuc + revisions: + - 876d26806584 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: busco + owner: iuc + revisions: + - 2babe6d5c561 + - 4e70d88adf2f + - c5a90fa4b8dd + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: ncbi_fcs_adaptor + owner: richard-burhans + revisions: + - d55ad8533d58 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: compleasm + owner: iuc + revisions: + - fc7334661489 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: helixer + owner: genouest + revisions: + - c2fc4ac35199 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation +- name: omark + owner: iuc + revisions: + - 0291e0e81551 + tool_panel_section_id: annotation + tool_panel_section_label: Annotation diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/assembly.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/assembly.yml index 296f1ca..b73c140 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/assembly.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/assembly.yml @@ -84,3 +84,33 @@ tools: owner: bgruening - name: bellerophon owner: iuc +- name: quast + owner: iuc +- name: megahit + owner: iuc +- name: metaspades + owner: nml +- name: merqury + owner: iuc +- name: meryl_count_kmers + owner: iuc +- name: meryl_groups_kmers + owner: iuc +- name: meryl_histogram_kmers + owner: iuc +- name: hifiasm + owner: bgruening +- name: pretext_map + owner: iuc +- name: pretext_graph + owner: iuc +- name: genomescope + owner: iuc +- name: yahs + owner: iuc +- name: pairtools_parse + owner: iuc +- name: pairtools_dedup + owner: iuc +- name: racon + owner: bgruening diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/assembly.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/assembly.yml.lock index 1aa390d..5c808f5 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/assembly.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/assembly.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -25,6 +25,7 @@ tools: owner: bgruening revisions: - 99ddbf037d98 + - bfab6f5b449d tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: mitobim @@ -205,8 +206,10 @@ tools: owner: bgruening revisions: - 0393c0415171 + - 3ef480892a9f - 50b6ec4074f4 - 5799092ffdff + - 59150c883ed5 tool_panel_section_id: assembly tool_panel_section_label: Assembly - name: velvet @@ -264,3 +267,101 @@ tools: - 321347bd0494 tool_panel_section_id: assembly tool_panel_section_label: Assembly +- name: quast + owner: iuc + revisions: + - 1b1cf0c96501 + - a3b35edea53a + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: megahit + owner: iuc + revisions: + - ab208c87d973 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: metaspades + owner: nml + revisions: + - f192c2fbe13f + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: merqury + owner: iuc + revisions: + - eb7b00ec347d + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: meryl_count_kmers + owner: iuc + revisions: + - bb6774c6aeaf + - e893b7452150 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: meryl_groups_kmers + owner: iuc + revisions: + - c4758f3bf36e + - cc8029eca6e9 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: meryl_histogram_kmers + owner: iuc + revisions: + - 9a0227fa7521 + - fa86bf923473 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: hifiasm + owner: bgruening + revisions: + - 5d365d5cbe9d + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: pretext_map + owner: iuc + revisions: + - 0346286a3b0a + - 9c942221e135 + - c6cec5ab35c1 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: pretext_graph + owner: iuc + revisions: + - 36ce83a739f2 + - 408ece2e4647 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: genomescope + owner: iuc + revisions: + - 460fad600dce + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: yahs + owner: iuc + revisions: + - 6756b34312cd + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: pairtools_parse + owner: iuc + revisions: + - a5876cca7b05 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: pairtools_dedup + owner: iuc + revisions: + - 3d1d241ceff2 + tool_panel_section_id: assembly + tool_panel_section_label: Assembly +- name: racon + owner: bgruening + revisions: + - 78c533842eeb + - e100a765370e + tool_panel_section_id: assembly + tool_panel_section_label: Assembly diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/bed.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/bed.yml.lock index 7f67621..9b915f7 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/bed.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/bed.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -6,6 +6,9 @@ tools: owner: iuc revisions: - 2892111d91f8 + - 64e2edfe7a2c + - a1a923cd89e8 + - a68aa6c1204a - b8348686a0b9 - dde39ba9c031 tool_panel_section_id: bed diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/biodiversity_data_exploration.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/biodiversity_data_exploration.yml.lock index 59ace81..304b942 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/biodiversity_data_exploration.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/biodiversity_data_exploration.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/chemicaltoolbox.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/chemicaltoolbox.yml index 45951d0..f1600c9 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/chemicaltoolbox.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/chemicaltoolbox.yml @@ -212,3 +212,11 @@ tools: owner: chemteam - name: gmx_rmsf owner: chemteam +- name: openbabel_compound_convert + owner: bgruening +- name: qcxms_neutral_run + owner: recetox +- name: qcxms_production_run + owner: recetox +- name: qcxms_getres + owner: recetox diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/chemicaltoolbox.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/chemicaltoolbox.yml.lock index 6fde2e8..baaa114 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/chemicaltoolbox.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/chemicaltoolbox.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -6,6 +6,7 @@ tools: owner: chemteam revisions: - 095ad4d096d1 + - a0c154146234 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: chembl @@ -17,6 +18,7 @@ tools: - name: ambertools_antechamber owner: chemteam revisions: + - 4fff93efc0f9 - 8a839e6a1e3e tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox @@ -90,6 +92,7 @@ tools: owner: chemteam revisions: - 070e3ecc3fda + - 1d4dd4f908d4 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: biomd_rmsd_clustering @@ -203,6 +206,7 @@ tools: owner: bgruening revisions: - 67ee76f0e497 + - bbbf5fb356dd tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: sdf_to_tab @@ -251,6 +255,7 @@ tools: owner: bgruening revisions: - 0993ac4f4a23 + - a1c53f0533b0 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox - name: qed @@ -403,6 +408,7 @@ tools: - name: gmx_merge_topology_files owner: chemteam revisions: + - 9389cd867cf2 - bc31d02be922 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox @@ -652,3 +658,28 @@ tools: - f261fded9631 tool_panel_section_id: chemicaltoolbox tool_panel_section_label: ChemicalToolBox +- name: openbabel_compound_convert + owner: bgruening + revisions: + - 4242b4d68e9c + - e2c36f62e22f + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: qcxms_neutral_run + owner: recetox + revisions: + - 475bbef634d4 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: qcxms_production_run + owner: recetox + revisions: + - cbe34f060712 + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox +- name: qcxms_getres + owner: recetox + revisions: + - 0109f244d25a + tool_panel_section_id: chemicaltoolbox + tool_panel_section_label: ChemicalToolBox diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/collection_operations.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/collection_operations.yml index a1be403..c29916a 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/collection_operations.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/collection_operations.yml @@ -8,3 +8,7 @@ tools: owner: nml - name: collection_element_identifiers owner: iuc +- name: split_file_to_collection + owner: bgruening +- name: pick_value + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/collection_operations.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/collection_operations.yml.lock index 9d1d893..c311d2b 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/collection_operations.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/collection_operations.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -18,6 +18,7 @@ tools: - name: collapse_collections owner: nml revisions: + - 830961c48e42 - 90981f86000f tool_panel_section_id: collection_operations tool_panel_section_label: Collection Operations @@ -27,3 +28,17 @@ tools: - d3c07d270a50 tool_panel_section_id: collection_operations tool_panel_section_label: Collection Operations +- name: split_file_to_collection + owner: bgruening + revisions: + - 2dae863c8f42 + - 6cbe2f30c2d7 + - baabc30154cd + tool_panel_section_id: collection_operations + tool_panel_section_label: Collection Operations +- name: pick_value + owner: iuc + revisions: + - b19e21af9c52 + tool_panel_section_id: collection_operations + tool_panel_section_label: Collection Operations diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/convert_formats.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/convert_formats.yml index 558b232..40bc899 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/convert_formats.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/convert_formats.yml @@ -50,3 +50,13 @@ tools: owner: iuc - name: xmlstarlet owner: ecology +- name: tooldistillator + owner: iuc +- name: tooldistillator_summarize + owner: iuc +- name: graphicsmagick_image_montage + owner: bgruening +- name: biom_convert + owner: iuc +- name: gffread + owner: devteam diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/convert_formats.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/convert_formats.yml.lock index 35afb67..bf51102 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/convert_formats.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/convert_formats.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -59,6 +59,7 @@ tools: owner: galaxyp revisions: - 331a50e8fd2f + - 6153e8ada1ee - ab6c14374bc0 - dd4ba10d0c45 tool_panel_section_id: convert_formats @@ -160,3 +161,36 @@ tools: - 4a9ac1df3278 tool_panel_section_id: convert_formats tool_panel_section_label: Convert Formats +- name: tooldistillator + owner: iuc + revisions: + - 9f1c8dc0253e + - c6b5c2975e51 + tool_panel_section_id: convert_formats + tool_panel_section_label: Convert Formats +- name: tooldistillator_summarize + owner: iuc + revisions: + - 3d0223265277 + - f4f71128f097 + tool_panel_section_id: convert_formats + tool_panel_section_label: Convert Formats +- name: graphicsmagick_image_montage + owner: bgruening + revisions: + - 601575b847c0 + - ab55af10f1ff + tool_panel_section_id: convert_formats + tool_panel_section_label: Convert Formats +- name: biom_convert + owner: iuc + revisions: + - d4d4e9febf5c + tool_panel_section_id: convert_formats + tool_panel_section_label: Convert Formats +- name: gffread + owner: devteam + revisions: + - 3e436657dcd0 + tool_panel_section_id: convert_formats + tool_panel_section_label: Convert Formats diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/deeptools.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/deeptools.yml.lock index ae99dc4..932f10d 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/deeptools.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/deeptools.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/emboss.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/emboss.yml.lock index d97824b..b2604ec 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/emboss.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/emboss.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/epigenetics.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/epigenetics.yml index 067d7c2..00f2920 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/epigenetics.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/epigenetics.yml @@ -28,3 +28,11 @@ tools: owner: bgruening - name: hicup2juicer owner: bgruening +- name: cooler_cload_tabix + owner: lldelisle +- name: cooler_balance + owner: lldelisle +- name: cooler_csort_tabix + owner: lldelisle +- name: cooler_makebins + owner: lldelisle diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/epigenetics.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/epigenetics.yml.lock index 9c13dc4..29b9be3 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/epigenetics.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/epigenetics.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -87,3 +87,31 @@ tools: - b4e7244246e2 tool_panel_section_id: epigenetics tool_panel_section_label: Epigenetics +- name: cooler_cload_tabix + owner: lldelisle + revisions: + - 0641e1c892c6 + - 168e86e96afa + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: cooler_balance + owner: lldelisle + revisions: + - 8f9fe0667b89 + - b387933e4d3d + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: cooler_csort_tabix + owner: lldelisle + revisions: + - 026950a1853c + - 8c3cba559c99 + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics +- name: cooler_makebins + owner: lldelisle + revisions: + - 3df254580b06 + - ebd2a52eb245 + tool_panel_section_id: epigenetics + tool_panel_section_label: Epigenetics diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/evolution.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/evolution.yml new file mode 100644 index 0000000..a19b047 --- /dev/null +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/evolution.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: Evolution +tools: +- name: iqtree + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/evolution.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/evolution.yml.lock new file mode 100644 index 0000000..138d1b6 --- /dev/null +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/evolution.yml.lock @@ -0,0 +1,12 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Evolution +tools: +- name: iqtree + owner: iuc + revisions: + - 18a61a9c1601 + - 6bbd30d58cf4 + tool_panel_section_id: evolution + tool_panel_section_label: Evolution diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/expression_tools.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/expression_tools.yml new file mode 100644 index 0000000..fce2868 --- /dev/null +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/expression_tools.yml @@ -0,0 +1,8 @@ +tool_panel_section_label: Expression Tools +tools: +- name: calculate_numeric_param + owner: iuc +- name: compose_text_param + owner: iuc +- name: map_param_value + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/expression_tools.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/expression_tools.yml.lock new file mode 100644 index 0000000..d09cdc1 --- /dev/null +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/expression_tools.yml.lock @@ -0,0 +1,23 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: Expression Tools +tools: +- name: calculate_numeric_param + owner: iuc + revisions: + - 0e586762f97b + tool_panel_section_id: expression_tools + tool_panel_section_label: Expression Tools +- name: compose_text_param + owner: iuc + revisions: + - e188c9826e0f + tool_panel_section_id: expression_tools + tool_panel_section_label: Expression Tools +- name: map_param_value + owner: iuc + revisions: + - 5ac8a4bf7a8d + tool_panel_section_id: expression_tools + tool_panel_section_label: Expression Tools diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/extract_features.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/extract_features.yml.lock index 078655d..4709ad7 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/extract_features.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/extract_features.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml index 44b26d0..17c0555 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml @@ -96,3 +96,27 @@ tools: owner: devteam - name: fastx_barcode_splitter owner: devteam +- name: seqkit_translate + owner: iuc +- name: fastp + owner: iuc +- name: cutadapt + owner: lparsons +- name: trimmomatic + owner: pjbriggs +- name: fastq_filter + owner: devteam +- name: fastqtofasta + owner: devteam +- name: fasta_compute_length + owner: devteam +- name: seqtk + owner: iuc +- name: ncbi_fcs_gx + owner: iuc +- name: rdeval + owner: richard-burhans +- name: mgnify_seqprep + owner: bgruening +- name: ncbi_blast_plus + owner: devteam diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml.lock index 9680d52..fed7dbb 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -6,6 +6,7 @@ tools: owner: devteam revisions: - 2c64fded1286 + - 5ec9f6bceaee tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: short_reads_trim_seq @@ -48,6 +49,7 @@ tools: - name: fasta_to_tabular owner: devteam revisions: + - 7e801ab2b70e - e7ed3c310b74 tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ @@ -264,6 +266,7 @@ tools: owner: devteam revisions: - 516b97a23d7e + - e773f1eb16cf tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ - name: fasta_nucleotide_changer @@ -302,3 +305,91 @@ tools: - 0b7ec11b3c7c tool_panel_section_id: fasta_fastq tool_panel_section_label: FASTA/FASTQ +- name: seqkit_translate + owner: iuc + revisions: + - 0e0b003c711f + - d35d114c26a7 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: fastp + owner: iuc + revisions: + - 10678d49d39e + - 1c183b0a6cfd + - 25c59c0ceb55 + - 281054a26e41 + - 3432a0e49b86 + - 65b93b623c77 + - a626e8c0e1ba + - c59d48774d03 + - dbf9c561ef29 + - f875da9d433c + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: cutadapt + owner: lparsons + revisions: + - 5eb7e84243f2 + - 80766b36005d + - 8e264b67a8c0 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: trimmomatic + owner: pjbriggs + revisions: + - b9aaed85cbd1 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: fastq_filter + owner: devteam + revisions: + - '144275714590' + - ff7d49ec777f + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: fastqtofasta + owner: devteam + revisions: + - 4a3e93647a4e + - ac3fed111eb6 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: fasta_compute_length + owner: devteam + revisions: + - 5cbde03c1103 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: seqtk + owner: iuc + revisions: + - 8511b6d85fc7 + - a019807f4e67 + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: ncbi_fcs_gx + owner: iuc + revisions: + - 5fe428757fab + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: rdeval + owner: richard-burhans + revisions: + - 37d67c252fed + - aef1eea2058c + tool_panel_section_id: fasta_fastq + tool_panel_section_label: FASTA/FASTQ +- name: mgnify_seqprep + owner: bgruening + revisions: + - 76ea9d4604bc + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized +- name: ncbi_blast_plus + owner: devteam + revisions: + - fc35ffc8c548 + tool_panel_section_id: ncbi_blast + tool_panel_section_label: NCBI Blast diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/fetch_alignments_sequences.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/fetch_alignments_sequences.yml.lock index 64b0cd3..6646925 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/fetch_alignments_sequences.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/fetch_alignments_sequences.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/filter_and_sort.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/filter_and_sort.yml.lock index 3fb4d3f..5b52f9f 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/filter_and_sort.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/filter_and_sort.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/gemini.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/gemini.yml.lock index 941f6ec..6b270a7 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/gemini.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/gemini.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/genome_editing.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/genome_editing.yml.lock index a169a7a..fd02abd 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/genome_editing.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/genome_editing.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/get_data.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/get_data.yml index 622d886..a870cf1 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/get_data.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/get_data.yml @@ -52,3 +52,7 @@ tools: owner: iuc - name: ega_download_client owner: iuc +- name: fastq_dl + owner: iuc +- name: uniprotxml_downloader + owner: galaxyp diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/get_data.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/get_data.yml.lock index bd838ab..35bb3b0 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/get_data.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/get_data.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -23,6 +23,7 @@ tools: - name: sra_tools owner: iuc revisions: + - 516a54ddf218 - 734abc7ac21d - 8848455c0270 - f5ea3ce9b9b0 @@ -173,3 +174,16 @@ tools: - 7d87a9d58aa1 tool_panel_section_id: get_data tool_panel_section_label: Get Data +- name: fastq_dl + owner: iuc + revisions: + - 3f1ee30e39e9 + - 41635d6d4738 + tool_panel_section_id: get_data + tool_panel_section_label: Get Data +- name: uniprotxml_downloader + owner: galaxyp + revisions: + - 4ddc8da62671 + tool_panel_section_id: get_data + tool_panel_section_label: Get Data diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/graph_display_data.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/graph_display_data.yml index 2d0d6cb..f08c54c 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/graph_display_data.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/graph_display_data.yml @@ -4,3 +4,23 @@ tools: owner: bgruening - name: plotly_parallel_coordinates_plot owner: bgruening +- name: bandage + owner: iuc +- name: ggplot2_heatmap + owner: iuc +- name: newick_utils + owner: iuc +- name: volcanoplot + owner: iuc +- name: ggplot2_heatmap2 + owner: iuc +- name: pe_histogram + owner: iuc +- name: pygenometracks + owner: iuc +- name: pretext_snapshot + owner: iuc +- name: ggplot2_point + owner: iuc +- name: jbrowse + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/graph_display_data.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/graph_display_data.yml.lock index ebef51b..1905312 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/graph_display_data.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/graph_display_data.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -15,3 +15,72 @@ tools: - 9958188c6195 tool_panel_section_id: graph_display_data tool_panel_section_label: Graph/Display Data +- name: bandage + owner: iuc + revisions: + - ddddce450736 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: ggplot2_heatmap + owner: iuc + revisions: + - 10515715c940 + - 15cebddc6dba + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: newick_utils + owner: iuc + revisions: + - b4163d2f64ab + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: volcanoplot + owner: iuc + revisions: + - 2f557f6abbfb + - 5e08a1e22dbc + - e4790edb4299 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: ggplot2_heatmap2 + owner: iuc + revisions: + - 48b42ee61bc5 + - 6a097d09fca3 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: pe_histogram + owner: iuc + revisions: + - 594b85e4237a + - bd1416eea1f0 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: pygenometracks + owner: iuc + revisions: + - 59fd173ac850 + - 86d0ebe09628 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: pretext_snapshot + owner: iuc + revisions: + - 0cc7a80463b9 + - 26f2fe7e53a1 + - 9ec9c22767c8 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: ggplot2_point + owner: iuc + revisions: + - 3b12bf9b4b87 + - f87634b12749 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data +- name: jbrowse + owner: iuc + revisions: + - a6e57ff585c0 + tool_panel_section_id: graph_display_data + tool_panel_section_label: Graph/Display Data diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/graphclust.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/graphclust.yml.lock index 72e1016..4a5eb62 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/graphclust.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/graphclust.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/hca_single_cell.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/hca_single_cell.yml.lock index d111e6c..2203198 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/hca_single_cell.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/hca_single_cell.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/hicexplorer.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/hicexplorer.yml.lock index 2feebae..07cb98b 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/hicexplorer.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/hicexplorer.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/imaging.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/imaging.yml index 9da10cf..0132b7d 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/imaging.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/imaging.yml @@ -4,3 +4,35 @@ tools: owner: imgteam - name: graphicsmagick_image_convert owner: bgruening +- name: 2d_simple_filter + owner: imgteam +- name: 2d_histogram_equalization + owner: imgteam +- name: 2d_auto_threshold + owner: imgteam +- name: bfconvert + owner: imgteam +- name: binary2labelimage + owner: imgteam +- name: overlay_images + owner: imgteam +- name: count_objects + owner: imgteam +- name: rename_tiff_channels + owner: goeckslab +- name: vitessce_spatial + owner: goeckslab +- name: squidpy_scatter + owner: goeckslab +- name: squidpy_spatial + owner: goeckslab +- name: imagemagick_image_montage + owner: bgruening +- name: scimap_mcmicro_to_anndata + owner: goeckslab +- name: scimap_phenotyping + owner: goeckslab +- name: backsub + owner: goeckslab +- name: scimap_plotting + owner: goeckslab diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/imaging.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/imaging.yml.lock index a46d734..0b662dc 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/imaging.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/imaging.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -16,3 +16,107 @@ tools: - 4e9a3745dce4 tool_panel_section_id: imaging tool_panel_section_label: Imaging +- name: 2d_simple_filter + owner: imgteam + revisions: + - d51310ab328a + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: 2d_histogram_equalization + owner: imgteam + revisions: + - b1c2c210813c + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: 2d_auto_threshold + owner: imgteam + revisions: + - 50fa6150e340 + - 699a5e9146b3 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: bfconvert + owner: imgteam + revisions: + - fcadded98e61 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: binary2labelimage + owner: imgteam + revisions: + - 7f8102bdbfa1 + - 984358e43242 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: overlay_images + owner: imgteam + revisions: + - 66fe62b96281 + - ca362a9bfa20 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: count_objects + owner: imgteam + revisions: + - b58447a2eed2 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: rename_tiff_channels + owner: goeckslab + revisions: + - 4763362914f4 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: vitessce_spatial + owner: goeckslab + revisions: + - 068da7f7cd83 + - 70c8be4d59e9 + - cab38f254824 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: squidpy_scatter + owner: goeckslab + revisions: + - b84c324b58bd + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: squidpy_spatial + owner: goeckslab + revisions: + - 2a5036c29889 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: imagemagick_image_montage + owner: bgruening + revisions: + - 506a90ab5581 + - 65703c06c1f6 + tool_panel_section_id: imaging + tool_panel_section_label: Imaging +- name: scimap_mcmicro_to_anndata + owner: goeckslab + revisions: + - 49c178651194 + - b1ead1b7e0aa + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized +- name: scimap_phenotyping + owner: goeckslab + revisions: + - 37dc4f51e827 + - 88fca6e905be + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized +- name: backsub + owner: goeckslab + revisions: + - bf9f98a7f936 + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized +- name: scimap_plotting + owner: goeckslab + revisions: + - 05a8d9dea3df + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/join__subtract_and_group.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/join__subtract_and_group.yml.lock index fac0ba2..3d59ee8 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/join__subtract_and_group.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/join__subtract_and_group.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -31,5 +31,7 @@ tools: owner: iuc revisions: - 4c07ddedc198 + - 562f3c677828 + - 61e2aa6bb55d tool_panel_section_id: join__subtract_and_group tool_panel_section_label: Join, Subtract and Group diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/mapping.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/mapping.yml index f346216..1a183e1 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/mapping.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/mapping.yml @@ -26,3 +26,13 @@ tools: owner: devteam - name: bwa_mem2 owner: iuc +- name: bowtie2 + owner: devteam +- name: minimap2 + owner: iuc +- name: rgrnastar + owner: iuc +- name: bwa + owner: devteam +- name: rna_starsolo + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/mapping.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/mapping.yml.lock index e6c116a..70a2fb5 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/mapping.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/mapping.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -78,7 +78,48 @@ tools: - name: bwa_mem2 owner: iuc revisions: + - af91699b8d4c - bec6ba059ded - bfaa0d22c2e4 tool_panel_section_id: mapping tool_panel_section_label: Mapping +- name: bowtie2 + owner: devteam + revisions: + - d5ceb9f3c25b + - f76cbb84d67f + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: minimap2 + owner: iuc + revisions: + - 539de907fd99 + - 5cc34c3f440d + - 66367287b4e6 + - 6945cd53bd2d + - 8c6cd2650d1f + - be1d967337e4 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: rgrnastar + owner: iuc + revisions: + - 53255f6eecfc + - de21b616f03a + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: bwa + owner: devteam + revisions: + - 1dfc975b48d5 + - 2477830927ec + - 64f11cf59c6e + - e188dc7a68e6 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping +- name: rna_starsolo + owner: iuc + revisions: + - a00cceb45700 + tool_panel_section_id: mapping + tool_panel_section_label: Mapping diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/metabolomics.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/metabolomics.yml index 02e299e..1492abd 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/metabolomics.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/metabolomics.yml @@ -74,3 +74,41 @@ tools: owner: workflow4metabolomics - name: matchms_similarity owner: recetox +- name: mfassignr_kmdnoise + owner: recetox +- name: mfassignr_histnoise + owner: recetox +- name: mfassignr_snplot + owner: recetox +- name: mfassignr_isofiltr + owner: recetox +- name: mfassignr_mfassigncho + owner: recetox +- name: mfassignr_recallist + owner: recetox +- name: mfassignr_findrecalseries + owner: recetox +- name: mfassignr_recal + owner: recetox +- name: mfassignr_mfassign + owner: recetox +- name: msnbase_readmsdata + owner: lecorguille +- name: xcms_plot_chromatogram + owner: lecorguille +- name: xcms_xcmsset + owner: lecorguille +- name: xcms_merge + owner: lecorguille +- name: xcms_group + owner: lecorguille +- name: xcms_retcor + owner: lecorguille +- name: intensity_checks + owner: melpetera +- name: xcms_fillpeaks + owner: lecorguille +- name: camera_annotate + owner: lecorguille +- name: table_pandas_rename_column + owner: recetox diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/metabolomics.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/metabolomics.yml.lock index ac94cd1..ff734e2 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/metabolomics.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/metabolomics.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -229,3 +229,119 @@ tools: - 872d8040f713 tool_panel_section_id: metabolomics tool_panel_section_label: Metabolomics +- name: mfassignr_kmdnoise + owner: recetox + revisions: + - a7a823839ae3 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_histnoise + owner: recetox + revisions: + - 9654573e6889 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_snplot + owner: recetox + revisions: + - f19c0631b9e5 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_isofiltr + owner: recetox + revisions: + - 1c199c3d5993 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_mfassigncho + owner: recetox + revisions: + - da64d663694b + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_recallist + owner: recetox + revisions: + - 6c7b17d38a1d + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_findrecalseries + owner: recetox + revisions: + - 1b4881c150cc + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_recal + owner: recetox + revisions: + - cfcf45ba58be + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: mfassignr_mfassign + owner: recetox + revisions: + - 22c80f584bb1 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: msnbase_readmsdata + owner: lecorguille + revisions: + - 35b6fe4d481c + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_plot_chromatogram + owner: lecorguille + revisions: + - 9291271ec4d9 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_xcmsset + owner: lecorguille + revisions: + - 3990a65b45a4 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_merge + owner: lecorguille + revisions: + - ae28a753a6f8 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_group + owner: lecorguille + revisions: + - 3820e3f3b1cb + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_retcor + owner: lecorguille + revisions: + - 33c0ca93f3ee + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: intensity_checks + owner: melpetera + revisions: + - 2e580585782e + - ec75de7f1e08 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: xcms_fillpeaks + owner: lecorguille + revisions: + - a8d866a71ba1 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: camera_annotate + owner: lecorguille + revisions: + - 75a1b3f7bacc + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics +- name: table_pandas_rename_column + owner: recetox + revisions: + - 3f54cd56a65e + - 8537763e4713 + tool_panel_section_id: metabolomics + tool_panel_section_label: Metabolomics diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/metagenomic_analysis.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/metagenomic_analysis.yml index ad4d581..be94114 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/metagenomic_analysis.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/metagenomic_analysis.yml @@ -62,3 +62,61 @@ tools: owner: iuc - name: mapseq owner: iuc +- name: checkm2 + owner: iuc +- name: kraken2 + owner: iuc +- name: bracken + owner: iuc +- name: recentrifuge + owner: iuc +- name: semibin + owner: iuc +- name: metabat2_jgi_summarize_bam_contig_depths + owner: iuc +- name: maxbin2 + owner: mbernt +- name: metabat2 + owner: iuc +- name: fasta_to_contig2bin + owner: iuc +- name: binette + owner: iuc +- name: drep_dereplicate + owner: iuc +- name: gtdbtk_classify_wf + owner: iuc +- name: coverm_genome + owner: iuc +- name: checkm_lineage_wf + owner: iuc +- name: coverm_contig + owner: iuc +- name: krakentools_kreport2krona + owner: iuc +- name: krakentools_extract_kraken_reads + owner: iuc +- name: ampvis2_load + owner: iuc +- name: dada2_plotqualityprofile + owner: iuc +- name: dada2_filterandtrim + owner: iuc +- name: dada2_learnerrors + owner: iuc +- name: dada2_dada + owner: iuc +- name: dada2_mergepairs + owner: iuc +- name: dada2_makesequencetable + owner: iuc +- name: dada2_removebimeradenovo + owner: iuc +- name: dada2_seqcounts + owner: iuc +- name: dada2_assigntaxonomyaddspecies + owner: iuc +- name: mash_paste + owner: iuc +- name: mash_dist + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/metagenomic_analysis.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/metagenomic_analysis.yml.lock index 5c57748..1d468bf 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/metagenomic_analysis.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/metagenomic_analysis.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -26,6 +26,7 @@ tools: owner: iuc revisions: - 43f9ca23c132 + - 9de5319ad2db tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis - name: sixgill @@ -196,3 +197,185 @@ tools: - f1d1dafc836d tool_panel_section_id: metagenomic_analysis tool_panel_section_label: Metagenomic Analysis +- name: checkm2 + owner: iuc + revisions: + - 304ac5b49dea + - 66acaec9f386 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: kraken2 + owner: iuc + revisions: + - 20e2f64aa1fe + - 241a78eb2935 + - e150ae930235 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: bracken + owner: iuc + revisions: + - 4d350ac5148e + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: recentrifuge + owner: iuc + revisions: + - 613ee22af97c + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: semibin + owner: iuc + revisions: + - afee33334a63 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: metabat2_jgi_summarize_bam_contig_depths + owner: iuc + revisions: + - 00e3b4ef7e0c + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: maxbin2 + owner: mbernt + revisions: + - 0917b2d6010d + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: metabat2 + owner: iuc + revisions: + - f375b4f6ef57 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: fasta_to_contig2bin + owner: iuc + revisions: + - fb2bed0eb02f + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: binette + owner: iuc + revisions: + - 37ab2cfedac4 + - 9053a39d7994 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: drep_dereplicate + owner: iuc + revisions: + - f54e7b3da33c + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: gtdbtk_classify_wf + owner: iuc + revisions: + - 53a019316350 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: coverm_genome + owner: iuc + revisions: + - 73b667038f46 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: checkm_lineage_wf + owner: iuc + revisions: + - c3735bcc9cb8 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: coverm_contig + owner: iuc + revisions: + - 28d740f2c0b0 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: krakentools_kreport2krona + owner: iuc + revisions: + - 02bbace216f2 + - 05e78a90e02d + - 2deaada69b14 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: krakentools_extract_kraken_reads + owner: iuc + revisions: + - 3b1963f729cb + - f329328da134 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: ampvis2_load + owner: iuc + revisions: + - 738474880da8 + - 9b3e1acc3ad0 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: dada2_plotqualityprofile + owner: iuc + revisions: + - 4e469b758915 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: dada2_filterandtrim + owner: iuc + revisions: + - 00e0347751b1 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: dada2_learnerrors + owner: iuc + revisions: + - a14a18a47c36 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: dada2_dada + owner: iuc + revisions: + - b35a5e8ff0fe + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: dada2_mergepairs + owner: iuc + revisions: + - 646c58820267 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: dada2_makesequencetable + owner: iuc + revisions: + - ebd632e95aae + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: dada2_removebimeradenovo + owner: iuc + revisions: + - efe26de231ec + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: dada2_seqcounts + owner: iuc + revisions: + - 390bc2645138 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: dada2_assigntaxonomyaddspecies + owner: iuc + revisions: + - 705d26fbea02 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: mash_paste + owner: iuc + revisions: + - e0c0fda064eb + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis +- name: mash_dist + owner: iuc + revisions: + - c932095af671 + tool_panel_section_id: metagenomic_analysis + tool_panel_section_label: Metagenomic Analysis diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/mimodd.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/mimodd.yml.lock index 389b08e..f3943cd 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/mimodd.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/mimodd.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/mothur.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/mothur.yml.lock index 2adc8d2..5e50506 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/mothur.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/mothur.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/multiple_alignments.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/multiple_alignments.yml index 9be965f..e7c1cfa 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/multiple_alignments.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/multiple_alignments.yml @@ -20,3 +20,9 @@ tools: owner: rnateam - name: cd_hit owner: iuc +- name: mmseqs2_easy_linclust_clustering + owner: iuc +- name: clustalw + owner: devteam +- name: mafft + owner: rnateam diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/multiple_alignments.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/multiple_alignments.yml.lock index 5c5d649..a180222 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/multiple_alignments.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/multiple_alignments.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -64,3 +64,22 @@ tools: - 7807800a3d03 tool_panel_section_id: multiple_alignments tool_panel_section_label: Multiple Alignments +- name: mmseqs2_easy_linclust_clustering + owner: iuc + revisions: + - b174c3405549 + tool_panel_section_id: multiple_alignments + tool_panel_section_label: Multiple Alignments +- name: clustalw + owner: devteam + revisions: + - 5b097fde95dd + tool_panel_section_id: multiple_alignments + tool_panel_section_label: Multiple Alignments +- name: mafft + owner: rnateam + revisions: + - 0a507f4bd19a + - 1233363389c1 + tool_panel_section_id: multiple_alignments + tool_panel_section_label: Multiple Alignments diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/nanopore.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/nanopore.yml.lock index a93ce19..93938bc 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/nanopore.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/nanopore.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -114,12 +114,14 @@ tools: - name: medaka_variant owner: iuc revisions: + - 0f5f4a208660 - eb746fa6f514 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: medaka_consensus_pipeline owner: iuc revisions: + - 79e9a869f40e - fc8804320156 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore @@ -159,13 +161,6 @@ tools: - c9218b9dc7f0 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore -- name: poretools_yield_plot - owner: iuc - revisions: - - 64a83664b814 - - c5c5a3e84989 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore - name: poretools_winner owner: iuc revisions: @@ -190,75 +185,44 @@ tools: - c1cbe2575d32 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore -- name: poretools_squiggle - owner: iuc - revisions: - - 26e6c9362b7b - - ce8af9373061 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore -- name: poretools_qualpos - owner: iuc - revisions: - - 2e22ebec211a - - 626b6c2be5c2 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore - name: poretools_qualdist owner: iuc revisions: - 72dfdbfab3cc tool_panel_section_id: nanopore tool_panel_section_label: Nanopore -- name: poretools_occupancy - owner: iuc - revisions: - - 0433aad600e9 - - 336791b5665f - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore - name: poretools_nucdist owner: iuc revisions: - 5c4fa65f5733 tool_panel_section_id: nanopore tool_panel_section_label: Nanopore -- name: poretools_hist - owner: iuc - revisions: - - 47936349f3e9 - - d1805f9c4c82 - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore - name: poretools_extract owner: iuc revisions: - 08064da7b7fb tool_panel_section_id: nanopore tool_panel_section_label: Nanopore -- name: poretools_events - owner: iuc - revisions: - - 1d835c691480 - - daf8518d243a - tool_panel_section_id: nanopore - tool_panel_section_label: Nanopore - name: nanoplot owner: iuc revisions: - 2a9afed42353 + - a02b8b3f5a0c tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: medaka_consensus owner: iuc revisions: - 18505fe2bdb1 + - db25ec99c3ea tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: flye owner: bgruening revisions: - 13e27b9094e8 + - 643e0ff70be5 + - cb8dfd28c16f tool_panel_section_id: nanopore tool_panel_section_label: Nanopore - name: pycoqc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/obo_ontology_manipulation.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/obo_ontology_manipulation.yml.lock index 157daae..12afd72 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/obo_ontology_manipulation.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/obo_ontology_manipulation.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/operate_on_genomic_intervals.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/operate_on_genomic_intervals.yml.lock index 457d88f..d90c074 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/operate_on_genomic_intervals.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/operate_on_genomic_intervals.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/other_tools.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/other_tools.yml.lock index 6ff530c..f31bb55 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/other_tools.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/other_tools.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/peak_calling.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/peak_calling.yml index 0d2208a..5420832 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/peak_calling.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/peak_calling.yml @@ -22,3 +22,5 @@ tools: owner: rnateam - name: dewseq owner: rnateam +- name: macs2 + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/peak_calling.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/peak_calling.yml.lock index 202184c..d7a3f18 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/peak_calling.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/peak_calling.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -70,3 +70,9 @@ tools: - e1cb2e012307 tool_panel_section_id: peak_calling tool_panel_section_label: Peak Calling +- name: macs2 + owner: iuc + revisions: + - 86e2413cf3f8 + tool_panel_section_id: peak_calling + tool_panel_section_label: Peak Calling diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/phenotype_association.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/phenotype_association.yml.lock index 0ecf7e2..43a5475 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/phenotype_association.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/phenotype_association.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml index cad879f..f0d3454 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml @@ -54,3 +54,9 @@ tools: owner: iuc - name: snp_dists owner: iuc +- name: pangolin + owner: iuc +- name: nextclade + owner: iuc +- name: fasttree + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml.lock index edf3054..992e6b0 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -178,3 +178,24 @@ tools: - f78492521996 tool_panel_section_id: phylogenetics tool_panel_section_label: Phylogenetics +- name: pangolin + owner: iuc + revisions: + - 2f1019071464 + - c12c7d0e067b + tool_panel_section_id: phylogenetics + tool_panel_section_label: Phylogenetics +- name: nextclade + owner: iuc + revisions: + - 128ba8da994f + - 4f6349228462 + tool_panel_section_id: phylogenetics + tool_panel_section_label: Phylogenetics +- name: fasttree + owner: iuc + revisions: + - bc939965ce41 + - e005e659ae21 + tool_panel_section_id: genome_diversity + tool_panel_section_label: Genome Diversity diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/picard.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/picard.yml.lock index 8f583bb..d178dfd 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/picard.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/picard.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -6,6 +6,8 @@ tools: owner: devteam revisions: - 3f254c5ced1d + - 881d7645d1bf + - a1f0b3f4b781 - ab1f60c26526 tool_panel_section_id: picard tool_panel_section_label: Picard diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/proteomics.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/proteomics.yml index ee04cb1..4834917 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/proteomics.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/proteomics.yml @@ -196,3 +196,23 @@ tools: owner: galaxyp - name: calisp owner: galaxyp +- name: maxquant + owner: galaxyp +- name: pepquery2 + owner: galaxyp +- name: metanovo + owner: galaxyp +- name: openms_decoydatabase + owner: galaxyp +- name: openms_featurefindermultiplex + owner: galaxyp +- name: openms_msgfplusadapter + owner: galaxyp +- name: openms_peptideindexer + owner: galaxyp +- name: openms_falsediscoveryrate + owner: galaxyp +- name: openms_idmapper + owner: galaxyp +- name: openms_metaprosip + owner: galaxyp diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/proteomics.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/proteomics.yml.lock index e23f95d..e7ab787 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/proteomics.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/proteomics.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -366,6 +366,7 @@ tools: owner: galaxyp revisions: - 3ec27b4cee7c + - a6ff76e057fd tool_panel_section_id: proteomics tool_panel_section_label: Proteomics - name: rawtools @@ -598,3 +599,63 @@ tools: - 867f17ede7f3 tool_panel_section_id: proteomics tool_panel_section_label: Proteomics +- name: maxquant + owner: galaxyp + revisions: + - 9c52362ae7bb + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: pepquery2 + owner: galaxyp + revisions: + - c32806a80862 + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: metanovo + owner: galaxyp + revisions: + - d6dcd3173bdf + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_decoydatabase + owner: galaxyp + revisions: + - 06cca574e337 + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_featurefindermultiplex + owner: galaxyp + revisions: + - c9b2a5022d9e + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_msgfplusadapter + owner: galaxyp + revisions: + - 810779f0cf49 + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_peptideindexer + owner: galaxyp + revisions: + - 0693b186f39e + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_falsediscoveryrate + owner: galaxyp + revisions: + - 4138acdeedfb + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_idmapper + owner: galaxyp + revisions: + - ea02403ff738 + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics +- name: openms_metaprosip + owner: galaxyp + revisions: + - 5f72a8fa935d + tool_panel_section_id: proteomics + tool_panel_section_label: Proteomics diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/qiime.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/qiime.yml.lock index 1d27e24..9df4a50 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/qiime.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/qiime.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/qiime_2.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/qiime_2.yml new file mode 100644 index 0000000..b0c6623 --- /dev/null +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/qiime_2.yml @@ -0,0 +1,34 @@ +tool_panel_section_label: QIIME 2 +tools: +- name: qiime2__demux__summarize + owner: q2d2 +- name: qiime2__demux__emp_paired + owner: q2d2 +- name: qiime2_core__tools__import + owner: q2d2 +- name: qiime2__demux__emp_single + owner: q2d2 +- name: qiime2__dada2__denoise_single + owner: q2d2 +- name: qiime2__feature_table__tabulate_seqs + owner: q2d2 +- name: qiime2__metadata__tabulate + owner: q2d2 +- name: qiime2__feature_table__summarize + owner: q2d2 +- name: qiime2__dada2__denoise_paired + owner: q2d2 +- name: qiime2__diversity__core_metrics_phylogenetic + owner: q2d2 +- name: qiime2__diversity__alpha_group_significance + owner: q2d2 +- name: qiime2__diversity__beta_group_significance + owner: q2d2 +- name: qiime2__fragment_insertion__sepp + owner: q2d2 +- name: qiime2__feature_classifier__classify_sklearn + owner: q2d2 +- name: qiime2__taxa__barplot + owner: q2d2 +- name: qiime2__diversity__alpha_rarefaction + owner: q2d2 diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/qiime_2.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/qiime_2.yml.lock new file mode 100644 index 0000000..1280063 --- /dev/null +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/qiime_2.yml.lock @@ -0,0 +1,117 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: QIIME 2 +tools: +- name: qiime2__demux__summarize + owner: q2d2 + revisions: + - 1a13e87462a0 + - 7f656fb2e7b6 + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__demux__emp_paired + owner: q2d2 + revisions: + - 8edb4dc16d6e + - 9f0c454cfc67 + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2_core__tools__import + owner: q2d2 + revisions: + - 52a1f79f0941 + - 8a0db69428c7 + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__demux__emp_single + owner: q2d2 + revisions: + - 0700d9de4f79 + - 8e01d149bcdb + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__dada2__denoise_single + owner: q2d2 + revisions: + - 1601b340fb81 + - 354f63459d37 + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__feature_table__tabulate_seqs + owner: q2d2 + revisions: + - a0b9e63b06c7 + - c4570ced1d88 + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__metadata__tabulate + owner: q2d2 + revisions: + - 40c226302c86 + - 9857be21dcaf + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__feature_table__summarize + owner: q2d2 + revisions: + - 4d8369756ee6 + - d0f2249afe30 + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__dada2__denoise_paired + owner: q2d2 + revisions: + - 933b92011b91 + - ff047d5ca265 + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__diversity__core_metrics_phylogenetic + owner: q2d2 + revisions: + - 7fc930fc43cf + - 9d7dd5419c37 + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__diversity__alpha_group_significance + owner: q2d2 + revisions: + - 6c0a2e0d1c9e + - 96988c25ca01 + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__diversity__beta_group_significance + owner: q2d2 + revisions: + - a0d20b8b681e + - c499a93403c7 + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__fragment_insertion__sepp + owner: q2d2 + revisions: + - 4342c148f53e + - a74f06287b8c + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__feature_classifier__classify_sklearn + owner: q2d2 + revisions: + - 771d8be25d7a + - b5ea3e026b8b + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__taxa__barplot + owner: q2d2 + revisions: + - 3da2f87501ee + - d29295070ccd + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 +- name: qiime2__diversity__alpha_rarefaction + owner: q2d2 + revisions: + - 22bfda174157 + - 6d56299524df + tool_panel_section_id: qiime_2 + tool_panel_section_label: QIIME 2 diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/quality_control.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/quality_control.yml index 8bf8a9f..e0dc487 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/quality_control.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/quality_control.yml @@ -2,3 +2,5 @@ tool_panel_section_label: Quality Control tools: - name: fastq_info owner: bgruening +- name: multiqc + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/quality_control.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/quality_control.yml.lock index b791405..0fe0325 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/quality_control.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/quality_control.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -8,3 +8,15 @@ tools: - 7a821cd57b43 tool_panel_section_id: quality_control tool_panel_section_label: Quality Control +- name: multiqc + owner: iuc + revisions: + - 31c42a2c02d3 + - 5e33b465d8d5 + - 9a913cdee30e + - a7e081ceb76a + - abfd8a6544d7 + - e4dd4c0622f6 + - f7e2f1eb3a16 + tool_panel_section_id: quality_control + tool_panel_section_label: Quality Control diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/rad_seq.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/rad_seq.yml.lock index 25c5c7b..6ebe2fe 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/rad_seq.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/rad_seq.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/rna_analysis.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/rna_analysis.yml index 3c7f279..c49b676 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/rna_analysis.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/rna_analysis.yml @@ -226,3 +226,17 @@ tools: owner: iuc - name: psiclass owner: iuc +- name: stringtie + owner: iuc +- name: brew3r_r + owner: iuc +- name: cufflinks + owner: devteam +- name: rseqc + owner: nilesh +- name: featurecounts + owner: iuc +- name: cmsearch_deoverlap + owner: rnateam +- name: edger + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/rna_analysis.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/rna_analysis.yml.lock index b2392d8..04af89e 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/rna_analysis.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/rna_analysis.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -691,3 +691,48 @@ tools: - 1b690aa060f6 tool_panel_section_id: rna_analysis tool_panel_section_label: RNA Analysis +- name: stringtie + owner: iuc + revisions: + - cbf488da3b2c + tool_panel_section_id: rna_analysis + tool_panel_section_label: RNA Analysis +- name: brew3r_r + owner: iuc + revisions: + - d3b0390f325f + tool_panel_section_id: rna_analysis + tool_panel_section_label: RNA Analysis +- name: cufflinks + owner: devteam + revisions: + - 6926716bbfb5 + tool_panel_section_id: rna_analysis + tool_panel_section_label: RNA Analysis +- name: rseqc + owner: nilesh + revisions: + - 27e16a30667a + tool_panel_section_id: rna_analysis + tool_panel_section_label: RNA Analysis +- name: featurecounts + owner: iuc + revisions: + - 30f6985f0ac7 + - 5dbff3a5845a + tool_panel_section_id: rna_analysis + tool_panel_section_label: RNA Analysis +- name: cmsearch_deoverlap + owner: rnateam + revisions: + - 42c5bf8ed1b0 + - 874ad23526a0 + tool_panel_section_id: rna_analysis + tool_panel_section_label: RNA Analysis +- name: edger + owner: iuc + revisions: + - ae2aad0a6d50 + - fd9902d118e5 + tool_panel_section_id: rna_analysis + tool_panel_section_label: RNA Analysis diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/sam_bam.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/sam_bam.yml index a80e1fe..c8ff766 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/sam_bam.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/sam_bam.yml @@ -30,3 +30,25 @@ tools: owner: devteam - name: samtools_coverage owner: iuc +- name: samtools_sort + owner: devteam +- name: bamtools_split_mapped + owner: iuc +- name: samtools_fastx + owner: iuc +- name: samtools_depth + owner: iuc +- name: samtools_view + owner: iuc +- name: qualimap_bamqc + owner: iuc +- name: bamtools_filter + owner: devteam +- name: samtools_idxstats + owner: devteam +- name: bamtools_split_ref + owner: iuc +- name: samtools_merge + owner: iuc +- name: samtools_stats + owner: devteam diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/sam_bam.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/sam_bam.yml.lock index c10d0ec..6ec0580 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/sam_bam.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/sam_bam.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -92,3 +92,88 @@ tools: - c4ff13d2aab3 tool_panel_section_id: sam_bam tool_panel_section_label: SAM/BAM +- name: samtools_sort + owner: devteam + revisions: + - 69dca890852c + - f2f2650aeade + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: bamtools_split_mapped + owner: iuc + revisions: + - fa7b5520ae53 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_fastx + owner: iuc + revisions: + - 491037bfc0d2 + - 66e23b11feae + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_depth + owner: iuc + revisions: + - 971dc85e9441 + - fb6d5ffc365f + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_view + owner: iuc + revisions: + - 0dbf49c414ae + - 32dc5f781059 + - 48bbbcb692ce + - 5826298f6a73 + - 5ec526530725 + - bf328cec6a42 + - c370440f901e + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: qualimap_bamqc + owner: iuc + revisions: + - 19ece8afbaab + - 30a201c9c310 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: bamtools_filter + owner: devteam + revisions: + - 62e4d6cdbaa7 + - 993b19f20c76 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_idxstats + owner: devteam + revisions: + - 13aad5cb9be4 + - fa5d3e61e429 + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: bamtools_split_ref + owner: iuc + revisions: + - 9b8feb118f9e + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_merge + owner: iuc + revisions: + - a7617eb92baf + - c8bc9d08b0e3 + - cae2794d2deb + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM +- name: samtools_stats + owner: devteam + revisions: + - 145f6d74ff5e + - 1cc79f49b8d5 + - 1ed8ed887035 + - 3a0efe14891f + - 541082d03bef + - 57934e90e27c + tool_panel_section_id: sam_bam + tool_panel_section_label: SAM/BAM diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/sanger_sequencing.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/sanger_sequencing.yml.lock index 95a7f69..af4388d 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/sanger_sequencing.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/sanger_sequencing.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/scanpy.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/scanpy.yml index ef4c6da..932746b 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/scanpy.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/scanpy.yml @@ -2,3 +2,5 @@ tool_panel_section_label: Scanpy tools: - name: scanpy_parameter_iterator owner: ebi-gxa +- name: anndata_ops + owner: ebi-gxa diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/scanpy.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/scanpy.yml.lock index 4926a0b..b6f3e86 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/scanpy.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/scanpy.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -9,3 +9,10 @@ tools: - 73d43034c860 tool_panel_section_id: scanpy tool_panel_section_label: Scanpy +- name: anndata_ops + owner: ebi-gxa + revisions: + - 7ef2403a250d + - a4774b7b2e85 + tool_panel_section_id: hca_scanpy + tool_panel_section_label: HCA-Scanpy diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/send_data.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/send_data.yml.lock index f766a8f..49b4ff7 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/send_data.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/send_data.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/single_cell.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/single_cell.yml index 0f4a151..477e1d7 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/single_cell.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/single_cell.yml @@ -32,3 +32,31 @@ tools: owner: artbio - name: cite_seq_count owner: iuc +- name: anndata_manipulate + owner: iuc +- name: baredsc_1d + owner: iuc +- name: baredsc_combine_1d + owner: iuc +- name: baredsc_2d + owner: iuc +- name: baredsc_combine_2d + owner: iuc +- name: anndata_import + owner: iuc +- name: anndata_inspect + owner: iuc +- name: scanpy_inspect + owner: iuc +- name: scanpy_filter + owner: iuc +- name: scanpy_normalize + owner: iuc +- name: scanpy_remove_confounders + owner: iuc +- name: scanpy_cluster_reduce_dimension + owner: iuc +- name: scanpy_plot + owner: iuc +- name: velocyto_cli + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/single_cell.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/single_cell.yml.lock index b7af2f6..7117db7 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/single_cell.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/single_cell.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -100,3 +100,97 @@ tools: - 3df3d1b51110 tool_panel_section_id: single_cell tool_panel_section_label: Single-cell +- name: anndata_manipulate + owner: iuc + revisions: + - 7e8c677a7b71 + - be1fdce914c6 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: baredsc_1d + owner: iuc + revisions: + - 769d815e4b0d + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: baredsc_combine_1d + owner: iuc + revisions: + - 5b7c81b35b89 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: baredsc_2d + owner: iuc + revisions: + - a90f8efe08b4 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: baredsc_combine_2d + owner: iuc + revisions: + - 02fc39c8610d + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: anndata_import + owner: iuc + revisions: + - 923dcc644832 + - d330b3082107 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: anndata_inspect + owner: iuc + revisions: + - 0bf7fddf90c7 + - afe044e6bc93 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_inspect + owner: iuc + revisions: + - 27c054e8d949 + - d86cb2ce311b + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_filter + owner: iuc + revisions: + - 8cb783c81905 + - 92a189c299d4 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_normalize + owner: iuc + revisions: + - 56c0d4acef02 + - e639abb0de92 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_remove_confounders + owner: iuc + revisions: + - 9fb627495ec2 + - be0d45c46e97 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_cluster_reduce_dimension + owner: iuc + revisions: + - 38db3fef7aad + - 49ce1315722c + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: scanpy_plot + owner: iuc + revisions: + - 0185bd174ea0 + - 16a1c3122996 + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell +- name: velocyto_cli + owner: iuc + revisions: + - 90e95e9ee190 + - f66590d0d3af + tool_panel_section_id: single_cell + tool_panel_section_label: Single-cell diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/spatial_omics.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/spatial_omics.yml index 59d2061..1ab966e 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/spatial_omics.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/spatial_omics.yml @@ -12,3 +12,5 @@ tools: owner: perssond - name: quantification owner: perssond +- name: mesmer + owner: goeckslab diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/spatial_omics.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/spatial_omics.yml.lock index 02a1442..bc28256 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/spatial_omics.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/spatial_omics.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -41,3 +41,9 @@ tools: - e11d5fafd0cc tool_panel_section_id: spatial_omics tool_panel_section_label: Spatial Omics +- name: mesmer + owner: goeckslab + revisions: + - 2675ff99a53b + tool_panel_section_id: spatial_omics + tool_panel_section_label: Spatial Omics diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/statistics.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/statistics.yml.lock index 6a99c0e..34722be 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/statistics.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/statistics.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/test_tools.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/test_tools.yml.lock index c36c31b..b2fae08 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/test_tools.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/test_tools.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/text_manipulation.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/text_manipulation.yml index 262a3a4..1174079 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/text_manipulation.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/text_manipulation.yml @@ -56,3 +56,11 @@ tools: owner: bgruening - name: add_value owner: devteam +- name: filter_tabular + owner: iuc +- name: query_tabular + owner: iuc +- name: text_processing + owner: bgruening +- name: concatenate_multiple_datasets + owner: artbio diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/text_manipulation.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/text_manipulation.yml.lock index feca6dd..bd04f9a 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/text_manipulation.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/text_manipulation.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -179,3 +179,36 @@ tools: - 023f0a3760b3 tool_panel_section_id: text_manipulation tool_panel_section_label: Text Manipulation +- name: filter_tabular + owner: iuc + revisions: + - 557ec8d7087d + - 90f657745fea + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: query_tabular + owner: iuc + revisions: + - cf34c344508d + - cf4397560712 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: text_processing + owner: bgruening + revisions: + - 3dc70b59608c + - 6073bb457ec0 + - 86755160afbf + - c41d78ae5fee + - d698c222f354 + - ddf54b12c295 + - f46f0e4f75c4 + - fbf99087e067 + tool_panel_section_id: text_manipulation + tool_panel_section_label: Text Manipulation +- name: concatenate_multiple_datasets + owner: artbio + revisions: + - 5b1b635232ed + tool_panel_section_id: uncategorized + tool_panel_section_label: Uncategorized diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/transcriptomics.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/transcriptomics.yml new file mode 100644 index 0000000..983a98f --- /dev/null +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/transcriptomics.yml @@ -0,0 +1,4 @@ +tool_panel_section_label: CellTypeScan +tools: +- name: decoupler_pseudobulk + owner: ebi-gxa diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/transcriptomics.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/transcriptomics.yml.lock new file mode 100644 index 0000000..cc6eb7f --- /dev/null +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/transcriptomics.yml.lock @@ -0,0 +1,12 @@ +install_repository_dependencies: false +install_resolver_dependencies: false +install_tool_dependencies: false +tool_panel_section_label: CellTypeScan +tools: +- name: decoupler_pseudobulk + owner: ebi-gxa + revisions: + - 2557d7869e78 + - ef054892d47f + tool_panel_section_id: celltypescan + tool_panel_section_label: CellTypeScan diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/variant_calling.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/variant_calling.yml index e7dcfce..cd01e1e 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/variant_calling.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/variant_calling.yml @@ -152,3 +152,13 @@ tools: owner: iuc - name: vcf2maf owner: iuc +- name: bcftools_norm + owner: iuc +- name: bcftools_consensus + owner: iuc +- name: lofreq_call + owner: iuc +- name: bcftools_annotate + owner: iuc +- name: freebayes + owner: devteam diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/variant_calling.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/variant_calling.yml.lock index 9759f24..2f05da2 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/variant_calling.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/variant_calling.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -91,6 +91,7 @@ tools: - name: snpsift owner: iuc revisions: + - 2e497a770bca - 5fab4f81391d - b04635ebfab0 tool_panel_section_id: variant_calling @@ -111,6 +112,7 @@ tools: owner: iuc revisions: - 7dfca164d2e3 + - 950d1d49d678 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: plink @@ -149,6 +151,7 @@ tools: owner: iuc revisions: - aa35ee7f3ab2 + - af7e416d8176 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling - name: lofreq_alnqual @@ -160,6 +163,8 @@ tools: - name: lofreq_indelqual owner: iuc revisions: + - 354b534eeab7 + - 426d707dfc47 - 971e07ca4456 tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling @@ -354,6 +359,8 @@ tools: - name: snpeff owner: iuc revisions: + - 6322be79bd8e + - 74aebe30fb52 - c7275bd8b4d6 - e8adfc4c0a6b tool_panel_section_id: variant_calling @@ -468,3 +475,39 @@ tools: - e8510e04a86a tool_panel_section_id: variant_calling tool_panel_section_label: Variant Calling +- name: bcftools_norm + owner: iuc + revisions: + - 271965b55437 + - 5fa262ce95dd + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: bcftools_consensus + owner: iuc + revisions: + - 8aa352093d73 + - 9a260f6fab93 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: lofreq_call + owner: iuc + revisions: + - b11e8e9c23bf + - e1461b5c52a0 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: bcftools_annotate + owner: iuc + revisions: + - 06eaadeffb7d + - 2c372041ed8c + - 403553ae19f6 + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling +- name: freebayes + owner: devteam + revisions: + - 0d8581534009 + - ef2c525bd8cd + tool_panel_section_id: variant_calling + tool_panel_section_label: Variant Calling diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/vcf_bcf.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/vcf_bcf.yml.lock index 7fd1465..b7163ed 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/vcf_bcf.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/vcf_bcf.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/virology.yml b/galaxy-qa1.galaxy.cloud.e-infra.cz/virology.yml index 33a43d6..28189fd 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/virology.yml +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/virology.yml @@ -2,3 +2,13 @@ tool_panel_section_label: Virology tools: - name: ivar_getmasked owner: iuc +- name: ivar_trim + owner: iuc +- name: ivar_variants + owner: iuc +- name: ivar_consensus + owner: iuc +- name: ivar_removereads + owner: iuc +- name: snipit + owner: iuc diff --git a/galaxy-qa1.galaxy.cloud.e-infra.cz/virology.yml.lock b/galaxy-qa1.galaxy.cloud.e-infra.cz/virology.yml.lock index b647b4e..5feda45 100644 --- a/galaxy-qa1.galaxy.cloud.e-infra.cz/virology.yml.lock +++ b/galaxy-qa1.galaxy.cloud.e-infra.cz/virology.yml.lock @@ -1,4 +1,4 @@ -install_repository_dependencies: true +install_repository_dependencies: false install_resolver_dependencies: false install_tool_dependencies: false tools: @@ -8,3 +8,41 @@ tools: - 2cf4a1cafc16 tool_panel_section_id: virology tool_panel_section_label: Virology +- name: ivar_trim + owner: iuc + revisions: + - 0893a1dbb807 + - 6606a8c97889 + - 7bd020da0ce5 + - c092052ed673 + tool_panel_section_id: virology + tool_panel_section_label: Virology +- name: ivar_variants + owner: iuc + revisions: + - 045d6d00f606 + - 1ef68546d37f + - 5e5dfc9e71e2 + tool_panel_section_id: virology + tool_panel_section_label: Virology +- name: ivar_consensus + owner: iuc + revisions: + - 17f911830a8c + - 1c5448133894 + - 253935875d96 + tool_panel_section_id: virology + tool_panel_section_label: Virology +- name: ivar_removereads + owner: iuc + revisions: + - 55a7867809f4 + - dec59e6af429 + tool_panel_section_id: virology + tool_panel_section_label: Virology +- name: snipit + owner: iuc + revisions: + - 877e80114d25 + tool_panel_section_id: virology + tool_panel_section_label: Virology