comparison multiIntersectBed.xml @ 1:82aac94b06c3 draft

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0:b8348686a0b9

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
        multiIntersectBed
        $header
        #if $zero.value == True:
            -empty
            -g ${chromInfo}
        #end if
        
        -i '$input1'
        '$input2'
        #for $q in $beds
            '${q.input}'
        #end for

        -names
        #if $name1.choice == "tag":
            '${input1.name}'
        #else
            '${name1.custom_name}'
        #end if

        #if $name2.choice == "tag":
            '${input2.name}'
        #else
            '${name2.custom_name}'
        #end if

        #for $q in $beds
            #if $q.name.choice == "tag":
                '${q.input.name}'
            #else
                '${q.input.custom_name}'
            #end if
        #end for
        &gt; '$output'
    </command>
    
    <inputs>
        <!-- Make it easy for the user, first two input files are always shown -->
        <!-- INPUT 1 -->
        <param name="input1" format="bed" type="data" label="First sorted BED file" />
        
        <conditional name="name1">
            <param name="choice" type="select" label="Sample name">
                <option value="tag" selected="true">Use input's tag</option>
                <option value="custom">Enter custom table name</option>
            </param>
            <when value="tag">
            </when>
            <when value="custom">
                <param name="custom_name" type="text" area="false" label="Custom sample name"/>
            </when>
        </conditional>

        <!-- INPUT 2 -->
        <param name="input2" format="bed" type="data" label="Second sorted BED file" />
        
        <conditional name="name2">
            <param name="choice" type="select" label="Sample name">
                <option value="tag" selected="true">Use input's tag</option>
                <option value="custom">Enter custom table name</option>
            </param>
            <when value="tag">
            </when>
            <when value="custom">
                <param name="custom_name" type="text" area="false" label="Custom sample name"/>
            </when>
        </conditional>

        <!-- Additional files, if the user needs more -->
        <repeat name="beds" title="Add'l sorted BED files" >
            <param name="input" format="bed" type="data" label="BED file" />

            <conditional name="name">
                <param name="choice" type="select" label="Sample name">
                    <option value="tag" selected="true">Use input's tag</option>
                    <option value="custom">Enter custom table name</option>
                </param>
                <when value="tag">
                </when>
                <when value="custom">
                    <param name="custom_name" type="text" area="false" label="Custom sample name"/>
                </when>
            </conditional>
        </repeat>

        <param name="header" type="boolean" checked="true" truevalue="-header" falsevalue="" label="Print header line" help="The first line will include the name of each sample." />

        <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" />

    </inputs>

    <outputs>
        <data format="tabular" name="output"  metadata_source="input1" label="Common intervals identified from among ${input1.name}, ${input2.name} and so on." />
    </outputs>
    <help>
    
**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. The pictorial and raw data examples below illustrate the behavior of this tool more clearly.


.. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/mbi.png


.. class:: warningmark

This tool requires that each BED file is reference-sorted (chrom, then start).

------

**Example input**::

    # a.bed
    chr1  6   12
    chr1  10  20
    chr1  22  27
    chr1  24  30
    
    # b.bed

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


@REFERENCES@

    </help>
    <expand macro="citations" />
</tool>

1:82aac94b06c3

        <import>macros.xml</import>
    </macros>
    <expand macro="requirements" />
    <expand macro="stdio" />
    <command>
<![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:
            -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="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" />

    </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="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[
**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.


.. class:: warningmark

This tool requires that each BED file is reference-sorted (chrom, then start).

------

**Example input**::

    # a.bed
    chr1  6   12bed
    chr1  10  20
    chr1  22  27
    chr1  24  30
    
    # b.bed

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


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