From f86534b100554ccffd770273179674ef82fd7317 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 19 May 2025 09:45:15 +0200
Subject: [PATCH 1/4] Added script to update all tools

---
 scripts/umsa_update_all.sh | 13 +++++++++++++
 1 file changed, 13 insertions(+)
 create mode 100644 scripts/umsa_update_all.sh

diff --git a/scripts/umsa_update_all.sh b/scripts/umsa_update_all.sh
new file mode 100644
index 0000000..a4d9500
--- /dev/null
+++ b/scripts/umsa_update_all.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+
+set -e
+
+TARGET_DIR="../galaxy-umsa.grid.cesnet.cz"
+
+for yml_file in "$TARGET_DIR"/*.yml; do
+    echo "Processing $yml_file"
+    python3 fix_lockfile.py "$yml_file"
+    python3 update_tool.py "$yml_file"
+done
+
+echo "All files processed."
\ No newline at end of file

From b7f19b7a26a876bd1c937884c252d4394147603f Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 19 May 2025 10:39:57 +0200
Subject: [PATCH 2/4] updated and moved tools

---
 .../post_processing.yml                       |  4 --
 .../post_processing.yml.lock                  | 10 -----
 galaxy-umsa.grid.cesnet.cz/recetox.yml.lock   |  3 ++
 galaxy-umsa.grid.cesnet.cz/visualization.yml  | 12 ++++++
 .../visualization.yml.lock                    | 43 +++++++++++++++++++
 galaxy-umsa.grid.cesnet.cz/w4m.yml            |  6 ++-
 galaxy-umsa.grid.cesnet.cz/w4m.yml.lock       | 19 +++++---
 galaxy-umsa.grid.cesnet.cz/xcms.yml           |  2 +
 galaxy-umsa.grid.cesnet.cz/xcms.yml.lock      |  6 +++
 9 files changed, 82 insertions(+), 23 deletions(-)
 delete mode 100644 galaxy-umsa.grid.cesnet.cz/post_processing.yml
 delete mode 100644 galaxy-umsa.grid.cesnet.cz/post_processing.yml.lock

diff --git a/galaxy-umsa.grid.cesnet.cz/post_processing.yml b/galaxy-umsa.grid.cesnet.cz/post_processing.yml
deleted file mode 100644
index 35c0507..0000000
--- a/galaxy-umsa.grid.cesnet.cz/post_processing.yml
+++ /dev/null
@@ -1,4 +0,0 @@
-tool_panel_section_label: Post-processing
-tools:
-- name: tablemerge
-  owner: melpetera
diff --git a/galaxy-umsa.grid.cesnet.cz/post_processing.yml.lock b/galaxy-umsa.grid.cesnet.cz/post_processing.yml.lock
deleted file mode 100644
index 7c8849c..0000000
--- a/galaxy-umsa.grid.cesnet.cz/post_processing.yml.lock
+++ /dev/null
@@ -1,10 +0,0 @@
-install_repository_dependencies: true
-install_resolver_dependencies: false
-install_tool_dependencies: false
-tools:
-- name: tablemerge
-  owner: melpetera
-  revisions:
-  - e44c5246247a
-  tool_panel_section_id: post_processing
-  tool_panel_section_label: Post-processing
diff --git a/galaxy-umsa.grid.cesnet.cz/recetox.yml.lock b/galaxy-umsa.grid.cesnet.cz/recetox.yml.lock
index 14a7c35..cac9a8d 100644
--- a/galaxy-umsa.grid.cesnet.cz/recetox.yml.lock
+++ b/galaxy-umsa.grid.cesnet.cz/recetox.yml.lock
@@ -45,6 +45,7 @@ tools:
   - 071a424241ec
   - 1a2aeb8137bf
   - 6480c6d5fa36
+  - 6fc9f6dbcef5
   - bf32ae95a06f
   tool_panel_section_id: recetox
   tool_panel_section_label: RECETOX
@@ -103,6 +104,7 @@ tools:
   owner: galaxyp
   revisions:
   - 19e45916daf9
+  - 5c04f9decc01
   tool_panel_section_id: recetox
   tool_panel_section_label: RECETOX
 - name: assign_ri_from_comment
@@ -160,5 +162,6 @@ tools:
   owner: recetox
   revisions:
   - 2b1118bce0b1
+  - 964b4559eb1b
   tool_panel_section_id: recetox
   tool_panel_section_label: RECETOX
diff --git a/galaxy-umsa.grid.cesnet.cz/visualization.yml b/galaxy-umsa.grid.cesnet.cz/visualization.yml
index 40690de..c1691f9 100644
--- a/galaxy-umsa.grid.cesnet.cz/visualization.yml
+++ b/galaxy-umsa.grid.cesnet.cz/visualization.yml
@@ -14,6 +14,18 @@ tools:
   owner: iuc
 - name: ggplot2_point
   owner: iuc
+- name: ggplot2_boxplot
+  owner: iuc
+- name: ggplot2_barplot
+  owner: iuc
+- name: seaborn
+  owner: iuc
+- name: seaborn_pairgrid
+  owner: iuc
+- name: upsetplot
+  owner: iuc
+- name: maplot
+  owner: iuc
 - name: rcx_boxplot
   owner: recetox
 - name: heatmap
diff --git a/galaxy-umsa.grid.cesnet.cz/visualization.yml.lock b/galaxy-umsa.grid.cesnet.cz/visualization.yml.lock
index ddf58fa..dcb3d44 100644
--- a/galaxy-umsa.grid.cesnet.cz/visualization.yml.lock
+++ b/galaxy-umsa.grid.cesnet.cz/visualization.yml.lock
@@ -13,6 +13,7 @@ tools:
   revisions:
   - 0e7290688b50
   - 17b666467c32
+  - 63d211052ffb
   - dfd5d981b5a4
   tool_panel_section_id: visualization
   tool_panel_section_label: Visualization
@@ -20,6 +21,7 @@ tools:
   owner: iuc
   revisions:
   - 10515715c940
+  - 15cebddc6dba
   - 1a72f938213e
   - 391a4cc45fea
   tool_panel_section_id: visualization
@@ -27,6 +29,7 @@ tools:
 - name: ggplot2_pca
   owner: iuc
   revisions:
+  - 1df3b30325dd
   - 7e616a1bdb07
   - ae344ccf9d62
   - b1268b7544d3
@@ -36,6 +39,7 @@ tools:
   owner: iuc
   revisions:
   - 398e5104f8a2
+  - 6b9816a913de
   - 6fc8bab811da
   - b0d96516e6a5
   tool_panel_section_id: visualization
@@ -54,6 +58,43 @@ tools:
   revisions:
   - 5298e06f14f9
   - e3a675da7fd0
+  - f87634b12749
+  tool_panel_section_id: visualization
+  tool_panel_section_label: Visualization
+- name: ggplot2_boxplot
+  owner: iuc
+  revisions:
+  - 653803fab921
+  tool_panel_section_id: visualization
+  tool_panel_section_label: Visualization
+- name: ggplot2_barplot
+  owner: iuc
+  revisions:
+  - 41e9114cc7cd
+  tool_panel_section_id: visualization
+  tool_panel_section_label: Visualization
+- name: seaborn
+  owner: iuc
+  revisions:
+  - 293a939f28c8
+  tool_panel_section_id: visualization
+  tool_panel_section_label: Visualization
+- name: seaborn_pairgrid
+  owner: iuc
+  revisions:
+  - 4a46d83cb08f
+  tool_panel_section_id: visualization
+  tool_panel_section_label: Visualization
+- name: upsetplot
+  owner: iuc
+  revisions:
+  - ec6141f6e5cb
+  tool_panel_section_id: visualization
+  tool_panel_section_label: Visualization
+- name: maplot
+  owner: iuc
+  revisions:
+  - e9212adafd7a
   tool_panel_section_id: visualization
   tool_panel_section_label: Visualization
 - name: rcx_boxplot
@@ -72,11 +113,13 @@ tools:
   owner: workflow4metabolomics
   revisions:
   - 51015f22fcb7
+  - cbedca3ba6e1
   tool_panel_section_id: visualization
   tool_panel_section_label: Visualization
 - name: xcms_plot_raw
   owner: workflow4metabolomics
   revisions:
   - 520448a32548
+  - 8b8d360316c3
   tool_panel_section_id: visualization
   tool_panel_section_label: Visualization
diff --git a/galaxy-umsa.grid.cesnet.cz/w4m.yml b/galaxy-umsa.grid.cesnet.cz/w4m.yml
index c4cf8cd..60fdf2d 100644
--- a/galaxy-umsa.grid.cesnet.cz/w4m.yml
+++ b/galaxy-umsa.grid.cesnet.cz/w4m.yml
@@ -1,10 +1,12 @@
 tool_panel_section_label: W4M
 tools:
-- name: xcms_refine
-  owner: workflow4metabolomics
 - name: qualitymetrics
   owner: ethevenot
 - name: bank_inhouse
   owner: fgiacomoni
 - name: batchcorrection
   owner: melpetera
+- name: tablemerge
+  owner: melpetera
+- name: checkformat
+  owner: ethevenot
\ No newline at end of file
diff --git a/galaxy-umsa.grid.cesnet.cz/w4m.yml.lock b/galaxy-umsa.grid.cesnet.cz/w4m.yml.lock
index cc07b98..83d617f 100644
--- a/galaxy-umsa.grid.cesnet.cz/w4m.yml.lock
+++ b/galaxy-umsa.grid.cesnet.cz/w4m.yml.lock
@@ -2,13 +2,6 @@ install_repository_dependencies: true
 install_resolver_dependencies: false
 install_tool_dependencies: false
 tools:
-- name: xcms_refine
-  owner: workflow4metabolomics
-  revisions:
-  - 090b33a9981c
-  - 6c2798bce3eb
-  tool_panel_section_id: w4m
-  tool_panel_section_label: W4M
 - name: qualitymetrics
   owner: ethevenot
   revisions:
@@ -27,3 +20,15 @@ tools:
   - 23314e1192d4
   tool_panel_section_id: w4m
   tool_panel_section_label: W4M
+- name: tablemerge
+  owner: melpetera
+  revisions:
+  - e44c5246247a
+  tool_panel_section_id: w4m
+  tool_panel_section_label: W4M
+- name: checkformat
+  owner: ethevenot
+  revisions:
+  - e7c5811ec12f
+  tool_panel_section_id: w4m
+  tool_panel_section_label: W4M
diff --git a/galaxy-umsa.grid.cesnet.cz/xcms.yml b/galaxy-umsa.grid.cesnet.cz/xcms.yml
index d0bebff..a04357a 100644
--- a/galaxy-umsa.grid.cesnet.cz/xcms.yml
+++ b/galaxy-umsa.grid.cesnet.cz/xcms.yml
@@ -18,3 +18,5 @@ tools:
   owner: lecorguille
 - name: xcms_export_samplemetadata
   owner: lecorguille
+- name: xcms_refine
+  owner: workflow4metabolomics
diff --git a/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock b/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock
index 2d528eb..da62e2f 100644
--- a/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock
+++ b/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock
@@ -74,3 +74,9 @@ tools:
   - e13c7bc91c63
   tool_panel_section_id: xcms
   tool_panel_section_label: XCMS
+- name: xcms_refine
+  owner: workflow4metabolomics
+  revisions:
+  - 6c2798bce3eb
+  tool_panel_section_id: xcms
+  tool_panel_section_label: XCMS

From e6766f03d7d48b91fd40ec7887a9d6289cadd372 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 19 May 2025 11:24:13 +0200
Subject: [PATCH 3/4] added missing revision

---
 galaxy-umsa.grid.cesnet.cz/xcms.yml.lock | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock b/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock
index da62e2f..0021507 100644
--- a/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock
+++ b/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock
@@ -76,7 +76,8 @@ tools:
   tool_panel_section_label: XCMS
 - name: xcms_refine
   owner: workflow4metabolomics
-  revisions:
+  revisions
+  - 090b33a9981c
   - 6c2798bce3eb
   tool_panel_section_id: xcms
   tool_panel_section_label: XCMS

From 80ac827a5f593f9784aaa8bdae995c856fd94f94 Mon Sep 17 00:00:00 2001
From: hechth <helge.hecht@recetox.muni.cz>
Date: Mon, 19 May 2025 11:24:56 +0200
Subject: [PATCH 4/4] fixed missing : and removed script

---
 galaxy-umsa.grid.cesnet.cz/xcms.yml.lock |  2 +-
 scripts/umsa_update_all.sh               | 13 -------------
 2 files changed, 1 insertion(+), 14 deletions(-)
 delete mode 100644 scripts/umsa_update_all.sh

diff --git a/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock b/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock
index 0021507..8c1a6e3 100644
--- a/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock
+++ b/galaxy-umsa.grid.cesnet.cz/xcms.yml.lock
@@ -76,7 +76,7 @@ tools:
   tool_panel_section_label: XCMS
 - name: xcms_refine
   owner: workflow4metabolomics
-  revisions
+  revisions:
   - 090b33a9981c
   - 6c2798bce3eb
   tool_panel_section_id: xcms
diff --git a/scripts/umsa_update_all.sh b/scripts/umsa_update_all.sh
deleted file mode 100644
index a4d9500..0000000
--- a/scripts/umsa_update_all.sh
+++ /dev/null
@@ -1,13 +0,0 @@
-#!/bin/bash
-
-set -e
-
-TARGET_DIR="../galaxy-umsa.grid.cesnet.cz"
-
-for yml_file in "$TARGET_DIR"/*.yml; do
-    echo "Processing $yml_file"
-    python3 fix_lockfile.py "$yml_file"
-    python3 update_tool.py "$yml_file"
-done
-
-echo "All files processed."
\ No newline at end of file