comparison multiIntersectBed.xml @ 34:dde39ba9c031 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bedtools commit b68002321ade5e160c556517a98ffb70f068be95

33:87ee588b3d45

<tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@WRAPPER_VERSION@">
    <description>identifies common intervals among multiple interval files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![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:
            -i
            #for $file in $tag.beds:
                "${file.input}"
            #end for
            -names
            #for $file in $tag.beds:
                "{$file.custom_name}"
            #end for
        #end if

        > '$output'
]]>
    </command>
    <inputs>
        <conditional name="tag">
            <param name="tag_select" type="select" label="Sample name">
                <option value="tag" selected="true">Use input's tag</option>
                <option value="custom">Enter custom name per file</option>
            </param>
            <when value="tag">
                <param name="inputs" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
            </when>
            <when value="custom">
                <repeat name="beds" title="Add BED files" min="2" >
                    <param name="input" format="@STD_BEDTOOLS_INPUTS@" type="data" multiple="True" label="@STD_BEDTOOLS_INPUT_LABEL@ 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" />

    </inputs>
    <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="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[
**What it does**

This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files.

    chr1	30	32	1	bob	    0	1	0
    chr1	32	34	1	sue	    0	0	1


@REFERENCES@
]]>
    </help>
    <expand macro="citations" />
</tool>

34:dde39ba9c031

<tool id="bedtools_multiintersectbed" name="bedtools Multiple Intersect" version="@TOOL_VERSION@+galaxy1">
    <description>identifies common intervals among multiple interval files</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command><![CDATA[
bedtools multiinter
$header
$cluster
-filler '${filler}'
$empty.empty_selector
@GENOME_FILE_UNION@

#if str($tag.tag_select) == "tag":
    -i
    #for $file in $tag.inputs
        '$file'
    #end for
#else:
    -i
    #for $file in $tag.beds:
        '${file.input}'
    #end for
    -names
    #for $file in $tag.beds:
        '{$file.custom_name}'
    #end for
#end if
> '$output'
    ]]></command>
    <inputs>
        <conditional name="tag">
            <param name="tag_select" type="select" label="Sample name">
                <option value="tag" selected="true">Use input's tag</option>
                <option value="custom">Enter custom name per file</option>
            </param>
            <when value="tag">
                <param name="inputs" type="data" format="@STD_BEDTOOLS_INPUTS@" multiple="true" label="@STD_BEDTOOLS_INPUT_LABEL@ files" />
            </when>
            <when value="custom">
                <repeat name="beds" title="Add BED files" min="2" >
                    <param name="input" type="data" format="@STD_BEDTOOLS_INPUTS@" label="@STD_BEDTOOLS_INPUT_LABEL@ file" />
                    <param name="custom_name" type="text" area="false" label="Custom sample name" />
                </repeat>
            </when>
        </conditional>
        <param argument="-cluster" type="boolean" truevalue="-cluster" falsevalue="" checked="false"
            label="Invoke Ryan Layers's clustering algorithm" />
        <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 argument="-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" />
        <expand macro="print_header" />
    </inputs>
    <outputs>
        <data name="output" format="bed" />
    </outputs>
    <tests>
        <test>
            <param name="tag_select" value="tag" />
            <param name="inputs" value="multiIntersectBed1.bed,multiIntersectBed2.bed,multiIntersectBed3.bed" ftype="bed" />

            <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[
**What it does**

This tool identifies common intervals among multiple, sorted BED files. Intervals can be common among 0 to N of the N input BED files.

    chr1	30	32	1	bob	    0	1	0
    chr1	32	34	1	sue	    0	0	1


@REFERENCES@
    ]]></help>
    <expand macro="citations" />
</tool>