comparison bcftools_gtcheck.xml @ 16:a29a2f40b665 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bcftools commit db275932cbb485cb44ae91e0b421d6f57698db49

15:5a321fab1fe4

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@">
    <description>Check sample identity</description>
    <macros>
        <token name="@EXECUTABLE@">gtcheck</token>
        <import>macros.xml</import>
    </macros>

  --genotypes '${section.genotypes}'
#end if

${section.all_sites}

#if $section.GTs_only:
  --GTs-only '${section.GTs_only}'
#end if

${section.homs_only}

#if $section.plot:
  --plot '${section.plot}'
#end if

        </section>
        <section name="sec_default" expanded="true" title="Default Options">
            <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
                   help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
            <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" />
            <param name="GTs_only" type="integer" label="Gts Only" value="99" optional="True" help="Use GTs, ignore PLs, using &lt;int&gt; for unseen genotypes" />
            <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
            <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" />
            <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" />
            <param name="plot" type="text" label="Plot" help="Prefix name for plot" />
        </section>

        <data name="output_file" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="view.vcf" />
            <param name="GTs_only" value="99" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="CN\t3\t10\t0\tNA00002\tNA00001"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[

16:a29a2f40b665

<?xml version='1.0' encoding='utf-8'?>
<tool name="bcftools @EXECUTABLE@" id="bcftools_@EXECUTABLE@" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
    <description>Check sample identity</description>
    <macros>
        <token name="@EXECUTABLE@">gtcheck</token>
        <import>macros.xml</import>
    </macros>

  --genotypes '${section.genotypes}'
#end if

${section.all_sites}

${section.homs_only}

#if $section.plot:
  --plot '${section.plot}'
#end if

        </section>
        <section name="sec_default" expanded="true" title="Default Options">
            <param name="genotypes" type="data" format="vcf,bcf" label="Genotypes to compare against" optional="True"
                   help="(-g) Checks sample identity or wehn omitted a multi-sample cross-check is performed"/>
            <param name="target_sample" type="text" label="Target Sample" optional="True" help="Target sample in the -g file (used only for plotting)" />
            <param name="all_sites" type="boolean" truevalue="--all-sites" falsevalue="" label="All Sites" help="Output comparison for all sites" />
            <param name="homs_only" type="boolean" truevalue="--homs-only" falsevalue="" label="Homs Only" help="Homozygous genotypes only (useful for low coverage data)" />
            <param name="query_sample" type="text" label="Query Sample" optional="True" help="Query sample (by default the first sample is checked)" />
            <param name="plot" type="text" label="Plot" help="Prefix name for plot" />
        </section>

        <data name="output_file" format="tabular" />
    </outputs>
    <tests>
        <test>
            <param name="input_file" ftype="vcf" value="view.vcf" />
            <output name="output_file">
                <assert_contents>
                    <has_text_matching expression="DC\tNA00002\tNA00001\t6"/>
                </assert_contents>
            </output>
        </test>
    </tests>
    <help><![CDATA[