Arc cwl

workflows/kallisto/kallisto-index.cwl

@@ -2,18 +2,42 @@
 cwlVersion: v1.2
 class: CommandLineTool
 
+label: Kallisto index
+doc: |
+  Builds a kallisto index
+
+  Usage: kallisto index [arguments] FASTA-files
+
+  Required argument:
+  -i, --index=STRING          Filename for the kallisto index to be constructed 
+
+  Optional argument:
+  -k, --kmer-size=INT         k-mer (odd) length (default: 31, max value: 63)
+  -t, --threads=INT           Number of threads to use (default: 1)
+  -d, --d-list=STRING         Path to a FASTA-file containing sequences to mask from quantification
+      --make-unique           Replace repeated target names with unique names
+      --aa                    Generate index from a FASTA-file containing amino acid sequences
+      --distinguish           Generate index where sequences are distinguished by the sequence name
+  -T, --tmp=STRING            Temporary directory (default: tmp)
+  -m, --min-size=INT          Length of minimizers (default: automatically chosen)
+  -e, --ec-max-size=INT       Maximum number of targets in an equivalence class (default: no maximum)
+
 hints:
   DockerRequirement:
     dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
   SoftwareRequirement:
     packages:
       kallisto:
-        version: [ "0.50.0" ]
-        specs: [ https://identifiers.org/biotools/kallisto ]
+        version: [ "0.51.1" ]
+        specs:
+          - https://identifiers.org/rrid/RRID:SCR_016582
+          - https://identifiers.org/biotools/kallisto 
 
 requirements:        
   - class: InlineJavascriptRequirement
 
+baseCommand: [kallisto, index]
+
 inputs:
   InputFiles:
     type: File[]
@@ -41,8 +65,6 @@ inputs:
     inputBinding:
       prefix: "--make-unique"
 
-baseCommand: [kallisto, index]
-
 outputs:
   index:
     type: File
@@ -51,5 +73,8 @@ outputs:
 
 $namespaces:
   edam: https://edamontology.org/
+  s: https://schema.org/
 $schemas:
   - https://edamontology.org/EDAM_1.18.owl
+
+s:license: https://spdx.org/licenses/BSD-2-Clause