Update tool versions and switch the https for EDAM

pvanheus · pvanheus · commit f6929e20e2f7 · 2022-10-16T10:47:12.000+02:00
diff --git a/conda/meta.yaml b/conda/meta.yaml
@@ -1,6 +1,6 @@
 {% set name = "lukasa" %}
-{% set version = "0.0.5" %}
-{% set sha256 = "095de485faea6bdf0e19f30ca6e7cdc037309499b24b4266c9d7013e9ad021f6" %}
+{% set version = "0.0.6" %}
+{% set sha256 = "1e6f311114a0fffd53398a2c8e5f3f735213c07c2fb5f7e8f72b1cd4dd7e98d7" %}
 
 package:
   name: {{ name|lower }}
diff --git a/galaxy/lukasa.xml b/galaxy/lukasa.xml
@@ -1,9 +1,9 @@
 <tool id="lukasa" name="Lukasa" version="@TOOL_VERSION@+galaxy0" python_template_version="3.5">
     <description>Align protein evidence against genomic contigs using metaeuk and spaln</description>
     <macros>
-        <token name="@TOOL_VERSION@">0.0.6</token>
+        <token name="@TOOL_VERSION@">0.0.8</token>
         <!-- note that this DOI is for lukasa 0.0.6 - update as needed -->
-        <token name="@DOI@">10.5281/zenodo.4084863</token> 
+        <token name="@DOI@">10.5281/zenodo.4084863</token>
     </macros>
     <requirements>
         <requirement type="package" version="@TOOL_VERSION@">lukasa</requirement>
@@ -16,24 +16,24 @@
             --output_filename '$output_gff' '$contigs_fasta' '$proteins_fasta'
     ]]></command>
     <inputs>
-        <param name='contigs_fasta' type='data' format='fasta' label='Genomic contigs (FASTA)' />
-        <param name='proteins_fasta' type='data' format='fasta' label='Proteins (FASTA)' />
-        <param name='species_table' type='text' label='Spaln species table to use (optional)' />
+        <param name="contigs_fasta" type="data" format="fasta" label="Genomic contigs (FASTA)"/>
+        <param name="proteins_fasta" type="data" format="fasta" label="Proteins (FASTA)"/>
+        <param name="species_table" type="text" label="Spaln species table to use (optional)"/>
     </inputs>
     <outputs>
-        <data name="output_gff" format='gff3' label='Map proteins to genome ${on_string}' />
+        <data name="output_gff" format="gff3" label="Map proteins to genome ${on_string}"/>
     </outputs>
     <tests>
         <test>
-            <param name="contigs_fasta" ftype="fasta" value="contig.fasta" />
-            <param name="proteins_fasta" ftype="fasta" value="proteins.fasta" />
-            <param name="species_table" value="cynosemi" />
-            <output name="output_gff" value="spaln_out.gff3" />
+            <param name="contigs_fasta" ftype="fasta" value="contig.fasta"/>
+            <param name="proteins_fasta" ftype="fasta" value="proteins.fasta"/>
+            <param name="species_table" value="cynosemi"/>
+            <output name="output_gff" value="spaln_out.gff3"/>
         </test>
         <test>
-            <param name="contigs_fasta" ftype="fasta" value="contig.fasta" />
-            <param name="proteins_fasta" ftype="fasta" value="proteins.fasta" />
-            <output name="output_gff" value="spaln_out_no_st.gff3" />
+            <param name="contigs_fasta" ftype="fasta" value="contig.fasta"/>
+            <param name="proteins_fasta" ftype="fasta" value="proteins.fasta"/>
+            <output name="output_gff" value="spaln_out_no_st.gff3"/>
         </test>
     </tests>
     <help><![CDATA[
@@ -50,4 +50,4 @@
     <citations>
         <citation type="doi">@DOI@</citation>
     </citations>
-</tool>
+</tool>
diff --git a/inputs/extract_regions.yml b/inputs/extract_regions.yml
@@ -8,7 +8,7 @@ region_file:
   path: /home/pvh/Documents/code/Masters/protein_evidence_mapping/data/proteins1.txt
 
 $namespaces:
-  edam: http://edamontology.org/
+  edam: https://edamontology.org/
   iana: https://www.iana.org/assignments/media-types/
 $schemas:
-  - http://edamontology.org/EDAM_1.18.owl
+  - https://edamontology.org/EDAM_1.18.owl
diff --git a/inputs/metaeuk_inputs.yml b/inputs/metaeuk_inputs.yml
@@ -9,6 +9,6 @@ query:
 output_name: test.fasta
 
 $namespaces:
-  edam: http://edamontology.org/
+  edam: https://edamontology.org/
 $schemas:
-  - http://edamontology.org/EDAM_1.18.owl
+  - https://edamontology.org/EDAM_1.18.owl
diff --git a/inputs/metaeuk_to_regions_inputs.yml b/inputs/metaeuk_to_regions_inputs.yml
@@ -4,6 +4,6 @@ metaeuk_fasta:
   format: edam:format_1929
 
 $namespaces:
-  edam: http://edamontology.org/
+  edam: https://edamontology.org/
 $schemas:
-  - http://edamontology.org/EDAM_1.18.owl
+  - https://edamontology.org/EDAM_1.18.owl
diff --git a/inputs/queue_workflow_inputs.yml b/inputs/queue_workflow_inputs.yml
@@ -9,6 +9,6 @@ proteins_fasta:
 species_table: cynosemi
   
 $namespaces:
-  edam: http://edamontology.org/
+  edam: https://edamontology.org/
 $schemas:
-  - http://edamontology.org/EDAM_1.18.owl
+  - https://edamontology.org/EDAM_1.18.owl
diff --git a/inputs/spaln_input.yml b/inputs/spaln_input.yml
@@ -10,6 +10,6 @@ species: cynosemi
 output_format: 0
 
 $namespaces:
-  edam: http://edamontology.org/
+  edam: https://edamontology.org/
 $schemas:
-  - http://edamontology.org/EDAM_1.18.owl
+  - https://edamontology.org/EDAM_1.18.owl
diff --git a/inputs/workflow1_inputs.yml b/inputs/workflow1_inputs.yml
@@ -13,6 +13,6 @@ metaeuk_output:
 species_table: cynosemi
 
 $namespaces:
-  edam: http://edamontology.org/
+  edam: https://edamontology.org/
 $schemas:
-  - http://edamontology.org/EDAM_1.18.owl
+  - https://edamontology.org/EDAM_1.18.owl
diff --git a/lukasa.py b/lukasa.py
@@ -20,9 +20,9 @@
 {}
 
 $namespaces:
-  edam: http://edamontology.org/
+  edam: https://edamontology.org/
 $schemas:
-  - http://edamontology.org/EDAM_1.18.owl
+  - https://edamontology.org/EDAM_1.18.owl
 """
 
 
diff --git a/tools/extract_regions.py b/tools/extract_regions.py
@@ -1,3 +1,5 @@
+#!/usr/bin/env python3
+
 from __future__ import print_function, division
 import sys
 
diff --git a/tools/metaeuk_easy_predict.cwl b/tools/metaeuk_easy_predict.cwl
@@ -1,15 +1,8 @@
 #!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
-
-hints:
-  SoftwareRequirement:
-    packages:
-      metaeuk:
-        version: [ "2.ddf2742" ]
-        specs: [ "https://github.com/soedinglab/metaeuk" ]
-  DockerRequirement:
-    dockerPull: quay.io/biocontainers/metaeuk:2.ddf2742--h2d02072_0
+$namespaces:
+  edam: http://edamontology.org/
 
 requirements:
   InlineJavascriptRequirement: {}
@@ -20,59 +13,57 @@ inputs:
     format: edam:format_1929
     inputBinding:
       position: 10
-  query:
-    type: File
-    format: edam:format_1929
-    inputBinding:
-      position: 20
-  output_name:
-    type: string
-    default: "metaeuk_output.fasta"
-    inputBinding:
-      position: 30
-  temp_dir:
-    type: string
-    default: ""
-    inputBinding:
-      valueFrom: "$(self ? self : runtime.tmpdir)"
-      position: 40
-  threads:
-    type: int?
+  eval:
+    type: float?
     inputBinding:
+      prefix: --metaeuk-eval
       position: 1
-      prefix: --threads
-  min_length:
-    type: int?
+  max_intron:
+    type: float?
     inputBinding:
+      prefix: --max-intron
       position: 1
-      prefix: --min-length
-  segment_eval:
+  min_coverage:
     type: float?
     inputBinding:
+      prefix: --metaeuk-tcov
       position: 1
-      prefix: -e
-  eval:
+  min_intron:
     type: float?
     inputBinding:
+      prefix: --min-intron
       position: 1
-      prefix: --metaeuk-eval
-  min_coverage:
-    type: float?
+  min_length:
+    type: int?
     inputBinding:
+      prefix: --min-length
       position: 1
-      prefix: --metaeuk-tcov
-  max_intron:
+  output_name:
+    type: string
+    default: metaeuk_output.fasta
+    inputBinding:
+      position: 30
+  query:
+    type: File
+    format: edam:format_1929
+    inputBinding:
+      position: 20
+  segment_eval:
     type: float?
     inputBinding:
+      prefix: -e
       position: 1
-      prefix: --max-intron
-  min_intron:
-    type: float?
+  temp_dir:
+    type: string
+    default: ''
+    inputBinding:
+      position: 40
+      valueFrom: '$(self ? self : runtime.tmpdir)'
+  threads:
+    type: int?
     inputBinding:
+      prefix: --threads
       position: 1
-      prefix: --min-intron
-
-baseCommand: [ metaeuk, easy-predict ]
 
 outputs:
   output_fasta:
@@ -81,7 +72,19 @@ outputs:
     outputBinding:
       glob: $(inputs.output_name)
 
-$namespaces:
-  edam: http://edamontology.org/
+baseCommand:
+- metaeuk
+- easy-predict
+
+hints:
+  DockerRequirement:
+    dockerPull: quay.io/biocontainers/metaeuk:6.a5d39d9--pl5321hf1761c0_1
+  SoftwareRequirement:
+    packages:
+      metaeuk:
+        specs:
+        - https://github.com/soedinglab/metaeuk
+        version:
+        - 6.a5d39d9--pl5321hf1761c0_1
 $schemas:
-  - http://edamontology.org/EDAM_1.18.owl
+- http://edamontology.org/EDAM_1.18.owl
diff --git a/tools/metaeuk_to_regions.cwl b/tools/metaeuk_to_regions.cwl
@@ -1,40 +1,30 @@
 #!/usr/bin/env cwl-runner
 cwlVersion: v1.0
 class: CommandLineTool
+$namespaces:
+  edam: http://edamontology.org/
+  iana: https://www.iana.org/assignments/media-types/
 
-# EDAM formats:
-# format_1929 - FASTA
-# format_1964 - plain text
-
-hints:
-  SoftwareRequirement:
-    packages: 
-      - package: python
-  DockerRequirement:
-    dockerPull: python:3.8-slim-buster
-    
 inputs:
-  scripts:
-    type: File
-    default:
-      class: File
-      basename: "extract_regions.py"
-      contents:
-        $include: "extract_regions.py"
+  fuzz_length:
+    doc: number of bases to add to the start and end of the region to extract
+    type: int?
     inputBinding:
-      position: 1
+      position: 3
   metaeuk_fasta:
     type: File
     format: edam:format_1929
     inputBinding:
       position: 2
-  fuzz_length:
-    type: int?
-    doc: number of bases to add to the start and end of the region to extract
+  scripts:
+    type: File
+    default:
+      class: File
+      basename: extract_regions.py
+      contents:
+        $include: extract_regions.py
     inputBinding:
-      position: 3
-
-baseCommand: [ python ]
+      position: 1
 
 outputs:
   contig_regions_files:
@@ -48,8 +38,14 @@ outputs:
     outputBinding:
       glob: proteins*.txt
 
-$namespaces:
-  edam: http://edamontology.org/
-  iana: https://www.iana.org/assignments/media-types/
+baseCommand:
+- python
+
+hints:
+  DockerRequirement:
+    dockerPull: python:3.10-slim-buster
+  SoftwareRequirement:
+    packages:
+    - package: python
 $schemas:
-  - http://edamontology.org/EDAM_1.18.owl
+- http://edamontology.org/EDAM_1.18.owl
diff --git a/tools/process_spaln_output.cwl b/tools/process_spaln_output.cwl
diff --git a/tools/samtools_faidx.cwl b/tools/samtools_faidx.cwl
diff --git a/tools/samtools_faidx_extract.cwl b/tools/samtools_faidx_extract.cwl
diff --git a/tools/spaln.cwl b/tools/spaln.cwl

Original file line number	Diff line number	Diff line change
`@@ -1,3 +1,5 @@`
	`1`	`+#!/usr/bin/env python3`
	`2`	`+`
`1`	`3`	`from __future__ import print_function, division`
`2`	`4`	`import sys`
`3`	`5`