comparison multiIntersectBed.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_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.0">
    <description>identifies common intervals among multiple interval files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

<![CDATA[
        bedtools multiinter
        $header
        $cluster
        -filler "${filler}"
        #if $zero.value == True:
            -empty
            -g $genome
        #end if

        #if str($tag.tag_select) == "tag":
            #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
            -i "${files}"
        #else:

                <param name="inputs" format="bed" type="data" multiple="True" label="BED files" />
            </when>
            <when value="custom">
                <repeat name="beds" title="Add BED files" min="2" >
                    <param name="input" format="bed" type="data" multiple="True" label="BED file" />
                    <param name="custom_name" type="text" area="false" label="Custom sample name"/>
                </repeat>
            </when>
        </conditional>
        <expand macro="genome" />
        <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue=""
            label="Invoke Ryan Layers's clustering algorithm"
            help="(-cluster)" />
        <param name="zero" type="boolean" checked="true"
            label="Report regions that are not covered by any of the files"
            help="If set, regions that are not overlapped by any file will also be reported. Requires a valid organism key for all input datasets" />
        <param name="filler" type="text" value="N/A"
            label="Text to use for no-coverage value"
            help="Can be 0.0, N/A, - or any other value. (-filler)" />
        <expand macro="print_header" />

    <outputs>
        <data format="bed" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="tag_select" value="tag"/>
            <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
            <param name="zero" value="False"/>
            <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="tag_select" value="tag"/>
            <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
            <param name="header" value="True"/>
            <param name="zero" value="False"/>
            <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" />
        </test>
        <test>
            <param name="tag_select" value="tag"/>
            <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
            <param name="zero" value="True"/>
            <param name="genome" value="multiIntersectBed1.len"/>
            <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[

17:44867b59dbf2

<tool id="bedtools_multiintersectbed" name="Multiple Intersect" version="@WRAPPER_VERSION@.1">
    <description>identifies common intervals among multiple interval files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />

<![CDATA[
        bedtools multiinter
        $header
        $cluster
        -filler "${filler}"
        $empty.empty_selector
        @GENOME_FILE_UNION@

        #if str($tag.tag_select) == "tag":
            #set files = '" "'.join( [ str( $file ) for $file in $tag.inputs ] )
            -i "${files}"
        #else:

                <param name="inputs" format="bed" type="data" multiple="True" label="BED files" />
            </when>
            <when value="custom">
                <repeat name="beds" title="Add BED files" min="2" >
                    <param name="input" format="bed" type="data" multiple="True" label="BED file" />
                    <param name="custom_name" type="text" area="false" label="Custom sample name" />
                </repeat>
            </when>
        </conditional>
        <param name="cluster" type="boolean" checked="false" truevalue="-cluster" falsevalue=""
            label="Invoke Ryan Layers's clustering algorithm"
            help="(-cluster)" />
        <conditional name="empty">
            <param name="empty_selector" argument="-empty" type="select" label="Report empty regions" help="Include regions that have zero coverage in all BedGraph datasets">
                <option value="-empty">Yes</option>
                <option value="">No</option>
            </param>
            <when value="-empty">
                <expand macro="input_conditional_genome_file" />
            </when>
            <when value="" />
        </conditional>
        <param name="filler" type="text" value="N/A"
            label="Text to use for no-coverage value"
            help="Can be 0.0, N/A, - or any other value. (-filler)" />
        <expand macro="print_header" />

    <outputs>
        <data format="bed" name="output" />
    </outputs>
    <tests>
        <test>
            <param name="tag_select" value="tag" />
            <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
            <param name="empty_selector" value="" />
            <output name="output" file="multiIntersectBed_result1.bed" ftype="bed" />
        </test>
        <test>
            <param name="tag_select" value="tag" />
            <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
            <param name="header" value="True" />
            <param name="empty_selector" value="" />
            <output name="output" file="multiIntersectBed_result2.bed" lines_diff="2" ftype="bed" />
        </test>
        <test>
            <param name="tag_select" value="tag" />
            <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />
            <param name="empty_selector" value="-empty" />
            <param name="genome_file_opts_selector" value="hist" />
            <param name="genome" value="multiIntersectBed1.len" />
            <output name="output" file="multiIntersectBed_result3.bed" ftype="bed" />
        </test>
    </tests>
    <help>
<![CDATA[