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Commit 2fb885ed authored by Dominik Brilhaus's avatar Dominik Brilhaus
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add metadata to kallisto

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1 merge request!19Arc cwl
Pipeline #9521 passed
Stage: arc_json
    Stage: quality_report_generator
      Stage: quality_report
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        workflows/kallisto/kallisto-index.cwl
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        ...@@ -2,18 +2,42 @@ ...@@ -2,18 +2,42 @@
        cwlVersion: v1.2 cwlVersion: v1.2
        class: CommandLineTool 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: hints:
        DockerRequirement: DockerRequirement:
        dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1 dockerPull: quay.io/biocontainers/kallisto:0.51.1--ha4fb952_1
        SoftwareRequirement: SoftwareRequirement:
        packages: packages:
        kallisto: kallisto:
        version: [ "0.50.0" ] version: [ "0.51.1" ]
        specs: [ https://identifiers.org/biotools/kallisto ] specs:
        - https://identifiers.org/rrid/RRID:SCR_016582
        - https://identifiers.org/biotools/kallisto
        requirements: requirements:
        - class: InlineJavascriptRequirement - class: InlineJavascriptRequirement
        baseCommand: [kallisto, index]
        inputs: inputs:
        InputFiles: InputFiles:
        type: File[] type: File[]
        ...@@ -41,8 +65,6 @@ inputs: ...@@ -41,8 +65,6 @@ inputs:
        inputBinding: inputBinding:
        prefix: "--make-unique" prefix: "--make-unique"
        baseCommand: [kallisto, index]
        outputs: outputs:
        index: index:
        type: File type: File
        ...@@ -51,5 +73,8 @@ outputs: ...@@ -51,5 +73,8 @@ outputs:
        $namespaces: $namespaces:
        edam: https://edamontology.org/ edam: https://edamontology.org/
        s: https://schema.org/
        $schemas: $schemas:
        - https://edamontology.org/EDAM_1.18.owl - https://edamontology.org/EDAM_1.18.owl
        s:license: https://spdx.org/licenses/BSD-2-Clause
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