comparison vcf2hrdetect.xml @ 8:b4dec06d8fc6 draft

"planemo upload for repository https://github.com/ARTbio/tools-artbio/tree/master/tools/lumpy_smoove commit 51dc6c56c7d95fc229ffee958354211cd454fd36"

7:8b0005fdfd04

<tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="1">
    <description>to tabular hrdetect</description>
    <macros>
        <import>macro_lumpy_smoove.xml</import>
    </macros>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />

    </outputs>

    <tests>
        <test>
            <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" />
            <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" ftype="tabular" />
        </test>
    </tests>
    <help>
**vcf2hrdetect** convert a vcf produced by lumpy-smoove to a somatic_sv.tsv tabular file compatible with
the HRDetect pipeline (https://github.com/eyzhao/hrdetect-pipeline/blob/master/data/example/patients/patient1/sample1/somatic_sv.tsv)

8:b4dec06d8fc6

<tool id="vcf2hrdetect" name="Convert lumpy-smoove vcf" version="2">
    <description>to tabular hrdetect</description>
    <requirements>
        <requirement type="package" version="0.2.5">smoove</requirement>
    </requirements>
    <macros>
        <import>macro_lumpy_smoove.xml</import>
    </macros>
    <stdio>
        <exit_code range="1:" level="fatal" description="Tool exception" />

    </outputs>

    <tests>
        <test>
            <param name="lumpy_smoove_vcf" value="test_vcf2hrdetect.vcf" ftype="vcf" />
            <output name="hrdetect_tabular" file="test_vcf2hrdetect.tab" sort="true" ftype="tabular" />
        </test>
    </tests>
    <help>
**vcf2hrdetect** convert a vcf produced by lumpy-smoove to a somatic_sv.tsv tabular file compatible with
the HRDetect pipeline (https://github.com/eyzhao/hrdetect-pipeline/blob/master/data/example/patients/patient1/sample1/somatic_sv.tsv)