add_helixer_workflow

workflows/genome_annotation/annotation-helixer/.dockstore.yml

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+version: 1.2
+workflows:
+- name: main
+  subclass: Galaxy
+  publish: true
+  primaryDescriptorPath: /Galaxy-Workflow-annotation_helixer.ga
+  testParameterFiles:
+  - /Galaxy-Workflow-annotation_helixer-tests.yml
+  authors:
+  - name: Romane Libouban
+    email: [email protected]
+    orcid: 0009-0001-4920-9951

workflows/genome_annotation/annotation-helixer/CHANGELOG.md

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+# Changelog
+
+## [0.1]
+
+Initial version of the Helixer workflow for genome annotation

workflows/genome_annotation/annotation-helixer/Galaxy-Workflow-annotation_helixer-tests.yml

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+- doc: Test outline for Helixer Workflow
+  job:
+    Genome sequence:
+      class: File
+      location: https://zenodo.org/records/13890774/files/genome_masked.fa?download=1
+      filetype: fasta
+
+  outputs:
+    helixer output:
+      location: https://zenodo.org/records/13890774/files/Helixer.gff3?download=1
+      compare: sim_size
+      delta: 300000
+
+    busco sum genome:
+      location: https://zenodo.org/records/13890774/files/Busco_short_summary_genome.txt?download=1
+      compare: sim_size
+      delta: 30000   
+    busco gff genome:
+      location: https://zenodo.org/records/13890774/files/Busco_GFF_genome.gff3?download=1
+      compare: sim_size
+      delta: 30000   
+    summary image genome:
+      location: https://zenodo.org/records/13890774/files/Busco_summary_image_genome.png?download=1
+      compare: sim_size
+      delta: 30000    
+    busco missing genome:
+      location: https://zenodo.org/records/13890774/files/Busco_missing_buscos_genome.tabular?download=1
+      compare: sim_size
+      delta: 30000    
+    busco table genome:
+      location: https://zenodo.org/records/13890774/files/Busco_full_table_genome.tabular?download=1
+      compare: sim_size
+      delta: 30000    
+
+    gffread peptides:
+      location: https://zenodo.org/records/13890774/files/gffread_pep.fasta?download=1
+      compare: sim_size
+      delta: 30000    
+
+    summary:
+      location: https://zenodo.org/records/13890774/files/genome_annotation_statistics_summary.txt?download=1
+      compare: sim_size
+      delta: 30000    
+    graphs:
+      location: https://zenodo.org/records/13890774/files/genome_annotation_statistics_graphs.pdf?download=1
+      compare: sim_size
+      delta: 30000       
+
+    summary image peptides:
+      location: https://zenodo.org/records/13902305/files/Busco_pep_summary_image.png?download=1
+      compare: sim_size
+      delta: 30000    
+    busco table peptides:
+      location: https://zenodo.org/records/13890774/files/Busco_full_table_pep.tabular?download=1
+      compare: sim_size
+      delta: 30000    
+    busco sum peptides:
+      location: https://zenodo.org/records/13890774/files/Busco_short_summary_pep.txt?download=1
+      compare: sim_size
+      delta: 30000    
+    busco gff peptides:
+      location: https://zenodo.org/records/13890774/files/Busco_GFF_pep.gff3?download=1
+      compare: sim_size
+      delta: 30000    
+    busco missing peptides:
+      location: https://zenodo.org/records/13890774/files/Busco_missing_buscos_pep.tabular?download=1
+      compare: sim_size
+      delta: 30000    
+
+    omark detail sum:
+      location: https://zenodo.org/records/14260288/files/OMArk_Detailed_summary_LUCA.txt?download=1
+      compare: sim_size
+      delta: 30000