comparison genomeCoverageBed.xml @ 17:44867b59dbf2 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit cf7a3674bc833bbd5fdd2ad02e724935ffc7a174

16:e0cec48a4695

<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 $input_type.input_type_select == 'bam'
            -ibam '$input_type.input'
        #else
            -i '$input_type.input'
            -g '$input_type.genome'
        #end if

        $split
        $strand

        #if str($report.report_select) == "bg":

                <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>

            <when value="bg">
                <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue=""
                    label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported.  (-bga)" />
                <param name="scale" type="float" value="1.0"
                    label="Scale the coverage by a constant factor"
                    help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)"/>
            </when>
            <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>

    </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>

17:44867b59dbf2

<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
        @GENOME_FILE_COVERAGE@

        $split
        $strand

        #if str($report.report_select) == "bg":

                <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="input_conditional_genome_file" />
            </when>
            <when value="bam">
                <param format="bam" name="input" type="data" label="BAM file" />
            </when>
        </conditional>

            <when value="bg">
                <param name="zero_regions" type="boolean" checked="False" truevalue="-bga" falsevalue=""
                    label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported.  (-bga)" />
                <param name="scale" type="float" value="1.0"
                    label="Scale the coverage by a constant factor"
                    help="Each bedGraph coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM). (-scale)" />
            </when>
            <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>

    </outputs>
    <tests>
        <test>
            <param name="input_type_select" value="bed" />
            <param name="input" value="genomeCoverageBed1.bed" ftype="bed" />
            <param name="genome_file_opts_selector" value="hist" />
            <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>