comparison mapBed.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_map" name="MapBed" version="@WRAPPER_VERSION@.0">
    <description>apply a function to a column for each overlapping interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools map
        -a "${inputA}"
        -b "${inputB}"
        $strand
        @C_AND_O_ARGUMENT@
        -f $overlap
        $reciprocal
        $split
        $header
        #if $genome.genome_choose == "-g" :
            -g $genome.genome
        #end if
        > "${output}"
]]>
    </command>
    <inputs>
        <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" />

            <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" />
        </expand>
        <expand macro="split" />
        <expand macro="print_header" />
        <conditional name="genome">
            <param name="genome_choose" type="boolean" checked="false" truevalue="-g" falsevalue=""
                label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="(-g)" />
            <when value="-g">
                <expand macro="genome" />
            </when>
            <when value="" />
        </conditional>
    </inputs>
    <outputs>
        <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}"/>
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="mapBed1.bed" ftype="bed" />
            <param name="inputB" value="mapBed2.bed" ftype="bed" />

                <param name="operation" value="collapse" />
            </repeat>
            <param name="strand" value="-s" />
            <output name="output" file="mapBed_result4.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**

17:44867b59dbf2

<tool id="bedtools_map" name="MapBed" version="@WRAPPER_VERSION@.1">
    <description>apply a function to a column for each overlapping interval</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![CDATA[
        bedtools map
        -a '${inputA}'
        -b '${inputB}'
        $strand
        @C_AND_O_ARGUMENT@
        -f $overlap
        $reciprocal
        $split
        $header
        @GENOME_FILE_MAPBED@
        > "${output}"
]]>
    </command>
    <inputs>
        <param format="bam,bed,vcf,gff,gff3" name="inputA" type="data" label="File A (BAM/BED/VCF/GFF)" />

            <param name="col" type="data_column" data_ref="inputA" label="Specify the column(s) that should be summarized" help="(-c)" />
        </expand>
        <expand macro="split" />
        <expand macro="print_header" />
        <conditional name="genome">
            <param name="genome_choose" argument="-g" type="select" 
                label="Specify a genome file the defines the expected chromosome order in the input files." >
                <option value="" selected="true">No</option>
                <option value="-g">Yes</option>
            </param>
            <when value="-g">
                <expand macro="input_conditional_genome_file" />
            </when>
            <when value="" />
        </conditional>
    </inputs>
    <outputs>
        <data format_source="inputA" name="output" metadata_source="inputA" label="Mapping of ${inputB.name} into ${inputA.name}" />
    </outputs>
    <tests>
        <test>
            <param name="inputA" value="mapBed1.bed" ftype="bed" />
            <param name="inputB" value="mapBed2.bed" ftype="bed" />

                <param name="operation" value="collapse" />
            </repeat>
            <param name="strand" value="-s" />
            <output name="output" file="mapBed_result4.bed" ftype="bed" />
        </test>
        <test>
            <param name="inputA" value="mapBed3.bed" ftype="bed" />
            <param name="inputB" value="mapBed4.bed" ftype="bed" />
            <repeat name="c_and_o_argument_repeat">
                <param name="col" value="5" />
                <param name="operation" value="collapse" />
            </repeat>
            <param name="strand" value="-s" />
            <param name="genome_choose" value="-g" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="mm9.len" ftype="bed" />
            <output name="output" file="mapBed_result5.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[
**What it does**