Add tools for IWC workflows

usegalaxy.org/annotation.yml

@@ -136,3 +136,7 @@ tools:
   owner: iuc
 - name: agat
   owner: bgruening
+- name: helixer
+  owner: genouest
+- name: omark
+  owner: iuc

usegalaxy.org/annotation.yml.lock

@@ -15,6 +15,7 @@ tools:
 - name: abricate
   owner: iuc
   revisions:
+  - 3f3e247c053d
   - 4efdca267d51
   - b734db305578
   - c2ef298da409
@@ -535,3 +536,15 @@ tools:
   - e7449b2c14bf
   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:
+  - 6f570ba54b41
+  tool_panel_section_id: annotation
+  tool_panel_section_label: Annotation

usegalaxy.org/assembly.yml.lock

@@ -1,4 +1,4 @@
-install_repository_dependencies: false
+install_repository_dependencies: true
 install_resolver_dependencies: false
 install_tool_dependencies: false
 tool_panel_section_label: Assembly

usegalaxy.org/bed.yml.lock

@@ -11,6 +11,7 @@ tools:
   - 64e2edfe7a2c
   - 7ab85ac5f64b
   - a1a923cd89e8
+  - a68aa6c1204a
   - b28e0cfa7ba1
   - ce3c7f062223
   - fe5b4cb8356c

usegalaxy.org/chemicaltoolbox.yml.lock

@@ -55,12 +55,14 @@ tools:
   owner: bgruening
   revisions:
   - 67ee76f0e497
+  - bbbf5fb356dd
   tool_panel_section_id: chemicaltoolbox
   tool_panel_section_label: ChemicalToolBox
 - name: ctb_rdkit_descriptors
   owner: bgruening
   revisions:
   - 0993ac4f4a23
+  - a1c53f0533b0
   tool_panel_section_id: chemicaltoolbox
   tool_panel_section_label: ChemicalToolBox
 - name: openbabel_compound_convert
@@ -81,6 +83,7 @@ tools:
   owner: chemteam
   revisions:
   - 070e3ecc3fda
+  - 1d4dd4f908d4
   - 2c349b027a01
   - 4da9ee404eab
   - a66c193fafdb
@@ -148,6 +151,7 @@ tools:
   - 04abdf96978b
   - 319a28774da9
   - 534ff13ea227
+  - 9389cd867cf2
   - bc31d02be922
   - d1d0efda35c0
   tool_panel_section_id: chemicaltoolbox

usegalaxy.org/convert_formats.yml.lock

@@ -242,11 +242,13 @@ tools:
   - 65a69de1e294
   - 8d6686664021
   - a7387ce2a8ca
+  - ea93df4b3df2
   tool_panel_section_id: convert_formats
   tool_panel_section_label: Convert Formats
 - name: tooldistillator_summarize
   owner: iuc
   revisions:
+  - 24eec94e6dfc
   - 6ff67d2860e1
   - def7a82d23e1
   - f3233d395549

usegalaxy.org/datamash.yml.lock

@@ -8,6 +8,7 @@ tools:
   revisions:
   - 2f3c6f2dcf39
   - 4c07ddedc198
+  - 562f3c677828
   - 746e8e4bf929
   tool_panel_section_id: datamash
   tool_panel_section_label: Datamash

usegalaxy.org/expression_tools.yml

@@ -1,8 +1,10 @@
 tool_panel_section_label: Expression Tools
 tools:
-  - name: compose_text_param
-    owner: iuc
-  - name: map_param_value
-    owner: iuc
-  - name: pick_value
-    owner: iuc
+- name: compose_text_param
+  owner: iuc
+- name: map_param_value
+  owner: iuc
+- name: pick_value
+  owner: iuc
+- name: calculate_numeric_param
+  owner: iuc

usegalaxy.org/expression_tools.yml.lock

@@ -24,3 +24,9 @@ tools:
   - b19e21af9c52
   tool_panel_section_id: expression_tools
   tool_panel_section_label: Expression Tools
+- name: calculate_numeric_param
+  owner: iuc
+  revisions:
+  - 0e586762f97b
+  tool_panel_section_id: expression_tools
+  tool_panel_section_label: Expression Tools

usegalaxy.org/fasta_fastq.yml.lock

@@ -48,6 +48,7 @@ tools:
   - c59d48774d03
   - d60c3f704da0
   - dbf9c561ef29
+  - dbfc505896e9
   tool_panel_section_id: fasta_fastq
   tool_panel_section_label: FASTA/FASTQ
 - name: fastx_trimmer

usegalaxy.org/graph_display_data.yml.lock

@@ -327,6 +327,7 @@ tools:
   - 0e592dcaeb7f
   - 137e08517410
   - 2fff478aca4b
+  - 49f3d3878413
   - 4aec47f872b3
   - 56f9a6e0fe80
   - 74074746ccd8

usegalaxy.org/imaging.yml

@@ -0,0 +1,16 @@
+tool_panel_section_label: Imaging
+tools:
+- 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

usegalaxy.org/imaging.yml.lock

@@ -0,0 +1,52 @@
+install_repository_dependencies: true
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tool_panel_section_label: Imaging
+tools:
+- name: 2d_simple_filter
+  owner: imgteam
+  revisions:
+  - d51310ab328a
+  - f70b215d155c
+  tool_panel_section_id: imaging
+  tool_panel_section_label: Imaging
+- name: 2d_histogram_equalization
+  owner: imgteam
+  revisions:
+  - 77f7159d775a
+  - b1c2c210813c
+  tool_panel_section_id: imaging
+  tool_panel_section_label: Imaging
+- name: 2d_auto_threshold
+  owner: imgteam
+  revisions:
+  - 3df9f0a4bf34
+  - 699a5e9146b3
+  tool_panel_section_id: imaging
+  tool_panel_section_label: Imaging
+- name: bfconvert
+  owner: imgteam
+  revisions:
+  - 85edbb7a436b
+  - fcadded98e61
+  tool_panel_section_id: imaging
+  tool_panel_section_label: Imaging
+- name: binary2labelimage
+  owner: imgteam
+  revisions:
+  - 984358e43242
+  tool_panel_section_id: imaging
+  tool_panel_section_label: Imaging
+- name: overlay_images
+  owner: imgteam
+  revisions:
+  - 37662cbf44b8
+  - 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

usegalaxy.org/metabolomics.yml

@@ -0,0 +1,6 @@
+tool_panel_section_label: Metabolomics
+tools:
+- name: metams_rungc
+  owner: yguitton
+- name: checkformat
+  owner: ethevenot

usegalaxy.org/metabolomics.yml.lock

@@ -0,0 +1,17 @@
+install_repository_dependencies: true
+install_resolver_dependencies: false
+install_tool_dependencies: false
+tool_panel_section_label: Metabolomics
+tools:
+- name: metams_rungc
+  owner: yguitton
+  revisions:
+  - 93508ea69eb5
+  tool_panel_section_id: metabolomics
+  tool_panel_section_label: Metabolomics
+- name: checkformat
+  owner: ethevenot
+  revisions:
+  - e7c5811ec12f
+  tool_panel_section_id: metabolomics
+  tool_panel_section_label: Metabolomics

usegalaxy.org/metagenomic_analysis.yml.lock

@@ -1,4 +1,4 @@
-install_repository_dependencies: false
+install_repository_dependencies: true
 install_resolver_dependencies: false
 install_tool_dependencies: false
 tool_panel_section_label: Metagenomic Analysis

usegalaxy.org/nanopore.yml

@@ -42,3 +42,5 @@ tools:
   owner: bgruening
 - name: pycoqc
   owner: iuc
+- name: clair3
+  owner: iuc

usegalaxy.org/nanopore.yml.lock

@@ -152,6 +152,7 @@ tools:
   - 84dcccebad3d
   - b2aae698b9d3
   - d6cddc06aeae
+  - db25ec99c3ea
   - eb1f4ba66dc6
   - fa11aa8103b2
   - fbf007713188
@@ -208,3 +209,10 @@ tools:
   - fae03f3d4bf7
   tool_panel_section_id: nanopore
   tool_panel_section_label: Nanopore
+- name: clair3
+  owner: iuc
+  revisions:
+  - 3843a30053ee
+  - 63e02ef6e153
+  tool_panel_section_id: nanopore
+  tool_panel_section_label: Nanopore

usegalaxy.org/picard.yml.lock

@@ -10,6 +10,7 @@ tools:
   - 3f254c5ced1d
   - 585027e65f3b
   - 7d34178f2812
+  - 881d7645d1bf
   - a1f0b3f4b781
   - b502c227b5e6
   - f9242e01365a

usegalaxy.org/sam_bam.yml

@@ -80,3 +80,5 @@ tools:
   owner: lldelisle
 - name: mosdepth
   owner: iuc
+- name: samtools_coverage
+  owner: iuc

usegalaxy.org/sam_bam.yml.lock

@@ -340,3 +340,9 @@ tools:
   - 5854d0da92b4
   tool_panel_section_id: sam_bam
   tool_panel_section_label: SAM/BAM
+- name: samtools_coverage
+  owner: iuc
+  revisions:
+  - c4ff13d2aab3
+  tool_panel_section_id: sam_bam
+  tool_panel_section_label: SAM/BAM