comparison vardict.xml @ 3:e0734e88a104 draft default tip

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/vardict commit 80e3742f499e8efabad1fe7627201466d0bdd190"

2:d262577e04b0

    <description>calls SNVs and indels for tumor-normal pairs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement>
        <requirement type="package" version="5.1.0">gawk</requirement>
        <requirement type="package" version="1.14">samtools</requirement>
    </requirements>
    <expand macro="stdio" />

        #if $interval_file:
            grep -w -f '$interval_file' ./ref.fa.fai > ./chromosomes.fa.fai &&
        #else
            ln -s ./ref.fa.fai ./chromosomes.fa.fai &&
        #end if
        awk 'BEGIN {FS=OFS="\t"} {print $1, "1", $2}' ./chromosomes.fa.fai > ./regions.bed &&

        vardict-java
        #if $select_mode.mode == "paired"
            -b "./tumor.bam|./normal.bam"
            -N 'Tumor'

            </conditional>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" ftype="fasta" value="genome.fasta" />
            </conditional>
            <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
            <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
        </test>
        <test expect_num_outputs="2">
            <conditional name="select_mode">

            </conditional>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="cached"/>
                <param name="ref_file" value="test_buildid"/>
            </conditional>
            <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
            <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
        </test>
        <test expect_num_outputs="2">
            <conditional name="select_mode">

3:e0734e88a104

    <description>calls SNVs and indels for tumor-normal pairs</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="3.10.2">python</requirement>
        <requirement type="package" version="@TOOL_VERSION@">vardict-java</requirement>
        <requirement type="package" version="5.1.0">gawk</requirement>
        <requirement type="package" version="1.14">samtools</requirement>
    </requirements>
    <expand macro="stdio" />

        #if $interval_file:
            grep -w -f '$interval_file' ./ref.fa.fai > ./chromosomes.fa.fai &&
        #else
            ln -s ./ref.fa.fai ./chromosomes.fa.fai &&
        #end if
        python '$__tool_directory__/split.py' ./chromosomes.fa.fai "\${VARDICT_CHUNKSIZE:-1000000}" "\${VARDICT_OVERLAP:-150}" > ./regions.bed &&

        vardict-java
        #if $select_mode.mode == "paired"
            -b "./tumor.bam|./normal.bam"
            -N 'Tumor'

            </conditional>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="history"/>
                <param name="ref_file" ftype="fasta" value="genome.fasta" />
            </conditional>

            <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
            <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
        </test>
        <test expect_num_outputs="2">
            <conditional name="select_mode">

            </conditional>
            <conditional name="reference_source">
                <param name="reference_source_selector" value="cached"/>
                <param name="ref_file" value="test_buildid"/>
            </conditional>

            <output name="all_variants" compare="re_match_multiline" file="all_variants_paired.vcf" />
            <output name="passed_variants" compare="re_match_multiline" file="passed_variants_paired.vcf" />
        </test>
        <test expect_num_outputs="2">
            <conditional name="select_mode">