tcga-vcf-reheader.xml

<tool id="tcga-vcf-reheader" name="TCGA VCF ReHeader" version="0.1">
    <description></description>

    <requirements>
        <container type="docker">tcgavcf-tool:0.1</container>
    </requirements>

    <command interpreter="python">
tcga-vcf-reheader.py ${input_vcf} ${output_vcf} ${config_yaml}
#if $sample.source == "file":
${sample.info_file}
#end if
    </command>

    <inputs>
        <param type="data" format="vcf" name="input_vcf" label="Input VCF"/>
        <param type="text" name="software_name" label="Software Name"/>
        <param type="text" name="software_version" label="Software Version"/>
        <param type="text" name="software_params" label="Software Params"/>
        <param type="text" name="center" label="Center"/>
        <conditional name="sample">
          <param type="select" name="source">
            <option value="manual">Manual</option>
            <option value="file">Sample Info File</option>
          </param>
          <when value="manual">
            <param type="text" name="reference_genome" label="Reference" size="50"/>
            <param type="text" name="platform" label="Platform" size="50" default="Illumina"/>
            <param type="text" name="participant_uuid" label="participant_uuid" size="50"/>
            <param type="text" name="disease_code" label="disease_code" default="XXXX"/>
            <param type="text" name="normal_analysis_uuid" label="Normal Analysis UUID" size="50"/>
            <param type="text" name="normal_bam_name" label="Normal Bam Name" size="50"/>
            <param type="text" name="normal_aliquot_uuid" label="Normal Aliquot UUID" size="50"/>
            <param type="text" name="normal_aliquot_barcode" label="Normal Aliquot Barcode" size="50"/>
            <param type="text" name="tumor_analysis_uuid" label="Tumor Analysis UUID" size="50"/>
            <param type="text" name="tumor_bam_name" label="Tumor Bam Name" size="50"/>
            <param type="text" name="tumor_aliquot_uuid" label="Tumor Aliquot UUID" size="50"/>
            <param type="text" name="tumor_aliquot_barcode" label="Tumor Aliquot Barcode" size="50"/>
          </when>
          <when value="file">
            <param type="data" format="txt" name="info_file" label="Sample Info"/>
          </when>
        </conditional>
    </inputs>

    <outputs>
        <data format="vcf" name="output_vcf" />
    </outputs>
    <configfiles>
        <configfile name="config_yaml"><![CDATA[
config:
    sample_line_format:
        SAMPLE=<
        ID={id},
        Description="{description}",
        SampleUUID={aliquot_uuid},SampleTCGABarcode={aliquot_barcode},
        AnalysisUUID={analysis_uuid},File="{bam_name}",
        Platform="{platform}",
        Source="dbGAP",Accession="dbGaP",
        softwareName=<{software_name}>,
        softwareVer=<{software_version}>,
        softwareParam=<{software_params}>
        >
    fixed_sample_params:
      software_name:      '${software_name}'
      software_version:   '${software_version}'
      software_params:    '"${software_params}"'
    fixed_headers:  # name, assert, value
        - [fileformat,  False,   'VCFv4.1']
        - [tcgaversion, False,   '1.1']
        - [phasing,     False,  'none']  # TODO: Think about this one.
        - [center,      False,  '"${center}"']
        - [vcfProcessLog,   False,  '<InputVCF=<${input_vcf}>, InputVCFSource=<${software_name}>,InputVCFVer=<4.1>, InputVCFParam=<"${software_params}">>']
#if $sample.source == "manual":
        - [participant_uuid,  False,  '${sample.participant_uuid}']
        - [disease_code, False, '${sample.disease_code}']
samples:
    NORMAL:
        description:     'Normal sample'
        analysis_uuid:   ${sample.normal_analysis_uuid}
        bam_name:        ${sample.normal_bam_name}
        aliquot_uuid:    ${sample.normal_aliquot_uuid}
        aliquot_barcode: ${sample.normal_aliquot_barcode}
        platform:        ${sample.platform}
    PRIMARY:
        description:    'Primary Tumor'
        analysis_uuid:  ${sample.tumor_analysis_uuid}
        bam_name:       ${sample.tumor_bam_name}
        aliquot_uuid:   ${sample.tumor_aliquot_uuid}
        aliquot_barcode:   ${sample.tumor_aliquot_barcode}
        platform:       ${sample.platform}
#end if
]]>
        </configfile>
    </configfiles>
    <help>

    </help>

    <tests>
    </tests>

</tool>