Merge branch 'main' into 20250716_hechth_tool_additions

Author: hechth

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:
@@ -420,24 +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:

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/metabolomics.yml

@@ -38,8 +38,6 @@ tools:
   owner: jfrancoismartin
 - name: asca
   owner: marie-tremblay-metatoul
-- name: bank_inhouse
-  owner: fgiacomoni
 - name: lcmsmatching
   owner: prog
 - name: golm_ws_lib_search

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

@@ -119,12 +119,6 @@ tools:
   - 93312041f1d5
   tool_panel_section_id: metabolomics
   tool_panel_section_label: Metabolomics
-- name: bank_inhouse
-  owner: fgiacomoni
-  revisions:
-  - 52798007c6b2
-  tool_panel_section_id: metabolomics
-  tool_panel_section_label: Metabolomics
 - name: lcmsmatching
   owner: prog
   revisions:

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 +178,3 @@ 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