GCZ - drop all cpt tools

galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml

@@ -124,24 +124,10 @@ tools:
   owner: bgruening
 - name: pfamscan
   owner: bgruening
-- name: cpt_phageqc_annotations
-  owner: cpt
-- name: cpt_intron_detection
-  owner: cpt
-- name: cpt_gbk_renumber
-  owner: cpt
-- name: cpt_require_shine
-  owner: cpt
 - name: tb_variant_filter
   owner: iuc
 - name: pharokka
   owner: iuc
-- name: cpt_gff_add_parents
-  owner: cpt
-- name: cpt_remove_annotations
-  owner: cpt
-- name: cpt_prep_for_apollo
-  owner: cpt
 - name: funannotate_predict
   owner: iuc
 - name: funannotate_compare

galaxy-qa1.galaxy.cloud.e-infra.cz/annotation.yml.lock

@@ -384,30 +384,6 @@ tools:
   - 15cff34c2005
   tool_panel_section_id: annotation
   tool_panel_section_label: Annotation
-- name: cpt_phageqc_annotations
-  owner: cpt
-  revisions:
-  - c3140b08d703
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_intron_detection
-  owner: cpt
-  revisions:
-  - 0a98d5259ef0
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_gbk_renumber
-  owner: cpt
-  revisions:
-  - 8cac332dbc77
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_require_shine
-  owner: cpt
-  revisions:
-  - a6dc48930318
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
 - name: tb_variant_filter
   owner: iuc
   revisions:
@@ -420,25 +396,6 @@ tools:
   - 2f40d2ccb0eb
   tool_panel_section_id: annotation
   tool_panel_section_label: Annotation
-- name: cpt_gff_add_parents
-  owner: cpt
-  revisions:
-  - d839cfd1c3a6
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_remove_annotations
-  owner: cpt
-  revisions:
-  - 49f50c55a9f8
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_prep_for_apollo
-  owner: cpt
-  revisions:
-  - 6901154b1003
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: funannotate_predict
   owner: iuc
   revisions:
   - 3cc3ef448854

galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml

@@ -96,5 +96,3 @@ tools:
   owner: devteam
 - name: fastx_barcode_splitter
   owner: devteam
-- name: cpt_fasta_remove_id
-  owner: cpt

galaxy-qa1.galaxy.cloud.e-infra.cz/fasta_fastq.yml.lock

@@ -302,9 +302,3 @@ tools:
   - 0b7ec11b3c7c
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
-- name: cpt_fasta_remove_id
-  owner: cpt
-  revisions:
-  - 78222649a59a
-  tool_panel_section_id: fasta_fastq
-  tool_panel_section_label: FASTA/FASTQ

galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml

@@ -54,7 +54,3 @@ tools:
   owner: iuc
 - name: snp_dists
   owner: iuc
-- name: cpt_related_genomes_nuc
-  owner: cpt
-- name: cpt_xmfa_to_table
-  owner: cpt

galaxy-qa1.galaxy.cloud.e-infra.cz/phylogenetics.yml.lock

@@ -178,15 +178,4 @@ tools:
   - f78492521996
   tool_panel_section_id: phylogenetics
   tool_panel_section_label: Phylogenetics
-- name: cpt_related_genomes_nuc
-  owner: cpt
-  revisions:
-  - 5a5fe0a6f78d
-  tool_panel_section_id: phylogenetics
-  tool_panel_section_label: Phylogenetics
-- name: cpt_xmfa_to_table
-  owner: cpt
-  revisions:
-  - 06d8e28d0bd7
-  tool_panel_section_id: phylogenetics
-  tool_panel_section_label: Phylogenetics
+

usegalaxy.cz/annotation.yml

@@ -240,50 +240,12 @@ tools:
   owner: iuc
 - name: braker3
   owner: genouest
-- name: cpt_phageqc_annotations
-  owner: cpt
-- name: cpt_gff_extract_seq
-  owner: cpt
-- name: cpt_intron_detection
-  owner: cpt
-- name: cpt_lipory
-  owner: cpt
-- name: cpt_gbk_renumber
-  owner: cpt
-- name: cpt_genome_editor
-  owner: cpt
-- name: cpt_annotation_table
-  owner: cpt
-- name: cpt_gff_rebase
-  owner: cpt
-- name: cpt_require_shine
-  owner: cpt
-- name: cpt_get_orfs
-  owner: cpt
-- name: cpt_gff_add_parents
-  owner: cpt
-- name: cpt_fix_sixpack
-  owner: cpt
-- name: cpt_shinefind
-  owner: cpt
-- name: cpt_type_filter
-  owner: cpt
-- name: cpt_req_phage_start
-  owner: cpt
-- name: cpt_remove_annotations
-  owner: cpt
-- name: cpt_prep_for_apollo
-  owner: cpt
-- name: cpt_convert_glimmer
-  owner: cpt
 - name: agat
   owner: bgruening
 - name: helixer
   owner: genouest
 - name: hmmer3
   owner: iuc
-- name: cpt_intersect_adjacent
-  owner: cpt
 - name: blast2go
   owner: peterjc
 - name: funannotate_predict

usegalaxy.cz/annotation.yml.lock

@@ -824,124 +824,6 @@ tools:
   - bd103884a09c
   tool_panel_section_id: annotation
   tool_panel_section_label: Annotation
-- name: cpt_phageqc_annotations
-  owner: cpt
-  revisions:
-  - c3140b08d703
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_gff_extract_seq
-  owner: cpt
-  revisions:
-  - 3d9f283ff09d
-  - ab40380424c9
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_intron_detection
-  owner: cpt
-  revisions:
-  - 0a98d5259ef0
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_lipory
-  owner: cpt
-  revisions:
-  - 2654bcd9b14d
-  - b79df4966ebb
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_gbk_renumber
-  owner: cpt
-  revisions:
-  - 8cac332dbc77
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_genome_editor
-  owner: cpt
-  revisions:
-  - 0e8079ac24f8
-  - 78ce8a1a8fd1
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_annotation_table
-  owner: cpt
-  revisions:
-  - 6998c2570145
-  - 848dd74f4382
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_gff_rebase
-  owner: cpt
-  revisions:
-  - 4f4b413056f6
-  - d0b52c1d6b25
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_require_shine
-  owner: cpt
-  revisions:
-  - a6dc48930318
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_get_orfs
-  owner: cpt
-  revisions:
-  - f56389d8abda
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_gff_add_parents
-  owner: cpt
-  revisions:
-  - d839cfd1c3a6
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_fix_sixpack
-  owner: cpt
-  revisions:
-  - 326429ea1d33
-  - e23a13d56fce
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_shinefind
-  owner: cpt
-  revisions:
-  - 6a5aac2a4c89
-  - 75f99d20c2a2
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_type_filter
-  owner: cpt
-  revisions:
-  - a77124b86382
-  - d40c9632250f
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_req_phage_start
-  owner: cpt
-  revisions:
-  - 33b5403e0357
-  - 4962f275bcaa
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_remove_annotations
-  owner: cpt
-  revisions:
-  - 49f50c55a9f8
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_prep_for_apollo
-  owner: cpt
-  revisions:
-  - 6901154b1003
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
-- name: cpt_convert_glimmer
-  owner: cpt
-  revisions:
-  - 746e52d94b49
-  - faff58a642fb
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
 - name: agat
   owner: bgruening
   revisions:
@@ -963,12 +845,6 @@ tools:
   - b5066aa77fea
   tool_panel_section_id: annotation
   tool_panel_section_label: Annotation
-- name: cpt_intersect_adjacent
-  owner: cpt
-  revisions:
-  - 7e393668b4b9
-  tool_panel_section_id: annotation
-  tool_panel_section_label: Annotation
 - name: blast2go
   owner: peterjc
   revisions:

usegalaxy.cz/convert_formats.yml

@@ -80,15 +80,3 @@ tools:
   owner: iuc
 - name: xmlstarlet
   owner: ecology
-- name: cpt_gff_split
-  owner: cpt
-- name: cpt_gbk_to_5col
-  owner: cpt
-- name: cpt_gff_to_gbk
-  owner: cpt
-- name: cpt_gbk_to_gff
-  owner: cpt
-- name: cpt_convert_mga
-  owner: cpt
-- name: cpt_fix_aragorn
-  owner: cpt

usegalaxy.cz/convert_formats.yml.lock

@@ -279,46 +279,4 @@ tools:
   revisions:
   - 4a9ac1df3278
   tool_panel_section_id: convert_formats
-  tool_panel_section_label: Convert Formats
-- name: cpt_gff_split
-  owner: cpt
-  revisions:
-  - 8bd03ba8510a
-  - ba8b6a5ffd9e
-  tool_panel_section_id: convert_formats
-  tool_panel_section_label: Convert Formats
-- name: cpt_gbk_to_5col
-  owner: cpt
-  revisions:
-  - 1bdd481d5c25
-  - 8f5f2142fc2b
-  tool_panel_section_id: convert_formats
-  tool_panel_section_label: Convert Formats
-- name: cpt_gff_to_gbk
-  owner: cpt
-  revisions:
-  - 03384dbb511d
-  - 35a6c466e270
-  tool_panel_section_id: convert_formats
-  tool_panel_section_label: Convert Formats
-- name: cpt_gbk_to_gff
-  owner: cpt
-  revisions:
-  - a921d6148d88
-  - bb6332a85aa6
-  tool_panel_section_id: convert_formats
-  tool_panel_section_label: Convert Formats
-- name: cpt_convert_mga
-  owner: cpt
-  revisions:
-  - 1bf722ba06e3
-  - 2c83f55438c9
-  tool_panel_section_id: convert_formats
-  tool_panel_section_label: Convert Formats
-- name: cpt_fix_aragorn
-  owner: cpt
-  revisions:
-  - 733cb0807083
-  - 8da37080e35f
-  tool_panel_section_id: convert_formats
-  tool_panel_section_label: Convert Formats
+  tool_panel_section_label: Convert Formats

usegalaxy.cz/fasta_fastq.yml

@@ -168,7 +168,5 @@ tools:
   owner: iuc
 - name: bbtools_bbmerge
   owner: iuc
-- name: cpt_fasta_remove_id
-  owner: cpt
 - name: prinseq
   owner: iuc

usegalaxy.cz/fasta_fastq.yml.lock

@@ -621,12 +621,6 @@ tools:
   - c9e516d65a3d
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
-- name: cpt_fasta_remove_id
-  owner: cpt
-  revisions:
-  - 78222649a59a
-  tool_panel_section_id: fasta_fastq
-  tool_panel_section_label: FASTA/FASTQ
 - name: prinseq
   owner: iuc
   revisions: