comparison genomeCoverageBed.xml @ 7:8e6b7c3597a8 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit 964b3159deeade1c90d20cef92dc15a14195edb7

6:d25966c8ddeb

<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.0">
    <description>compute the coverage over an entire genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools genomecov
        #if $input.ext == "bam"
            -ibam '$input'
        #else
            -i '$input'
            -g $genome
        #end if

        $split
        $strand

        > '$output'
]]>
    </command>
    <inputs>
        <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed">
              <validator type="unspecified_build" />
        </param>
        <conditional name="report">
            <param name="report_select" type="select" label="Output type">
                <option value="bg" selected="true">BedGraph coverage file</option>
                <option value="hist">Data suiteable for Histogram</option>
            </param>

            <when value="hist">
                <param name="max" type="integer" label="Specify max depth" value="0"
                    help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/>
            </when>
        </conditional>
        <expand macro="genome" />
        <expand macro="split" />
        <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)">
            <option value="">both strands combined</option>
            <option value="-strand +">positive strand only</option>
            <option value="-strand -">negative strand only</option>

            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
            <param name="genome" value="genomeCoverageBed1.len" />
            <param name="report_select" value="hist" />
            <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
        </test>
    </tests>
    <help>

7:8e6b7c3597a8

<tool id="bedtools_genomecoveragebed" name="Genome Coverage" version="@WRAPPER_VERSION@.1">
    <description>compute the coverage over an entire genome</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools genomecov
        #if $input_type.input_type_select == 'bam'
            -ibam '$input_type.input'
        #else
            -i '$input_type.input'
            -g '$input_type.genome'
        #end if

        $split
        $strand

        > '$output'
]]>
    </command>
    <inputs>
        <conditional name="input_type">
            <param name="input_type_select" type="select" label="Input type">
                <option value="bed">BED/VCF/GFF</option>
                <option value="bam">BAM</option>
            </param>
            <when value="bed">
                <param format="bed,vcf,gff,gff3" name="input" type="data" label="BED/VCF/GFF file" />
                <expand macro="genome" />
            </when>
            <when value="bam">
                <param format="bam" name="input" type="data" label="BAM file" />
            </when>
        </conditional>
        <conditional name="report">
            <param name="report_select" type="select" label="Output type">
                <option value="bg" selected="true">BedGraph coverage file</option>
                <option value="hist">Data suiteable for Histogram</option>
            </param>

            <when value="hist">
                <param name="max" type="integer" label="Specify max depth" value="0"
                    help="Combine all positions with a depth >= max into a single bin in the histogram. (-max)"/>
            </when>
        </conditional>
        <expand macro="split" />
        <param name="strand" type="select" label="Calculate coverage based on" help="(-strand)">
            <option value="">both strands combined</option>
            <option value="-strand +">positive strand only</option>
            <option value="-strand -">negative strand only</option>

            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="input_type_select" value="bed" />
            <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
            <param name="genome" value="genomeCoverageBed1.len" ftype="tabular" />
            <param name="report_select" value="hist" />
            <output name="output" file="genomeCoverageBed_result1.bed" ftype="tabular" />
        </test>
    </tests>
    <help>