<tool id="bedtools_multiintersectbed" name="Intersect multiple sorted BED files" version="@WRAPPER_VERSION@.0">
    <description></description>
    <macros>
        <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).


.. class:: infomark

The output file will contain five fixed columns, plus additional columns for each BED file:

    * 1. Chromosome name (or 'genome' for whole-genome coverage).
    * 2. The zero-based start position of the interval.
    * 3. The one-based end position of the interval.
    * 4. The number of input files that had at least one feature overlapping this interval.
    * 5. A list of input files or labels that had at least one feature overlapping this interval.
    * 6. For each input file, an indication (1 = Yes, 0 = No) of whether or not the file had at least one feature overlapping this interval.

------

**Example input**::

    # a.bed
    chr1  6   12
    chr1  10  20
    chr1  22  27
    chr1  24  30
    
    # b.bed
    chr1  12  32
    chr1  14  30
    
    # c.bed
    chr1  8   15
    chr1  10  14
    chr1  32  34


------

**Example without a header and without reporting intervals with zero coverage**::


    chr1	6	8	1	1	1	0	0
    chr1	8	12	2	1,3	1	0	1
    chr1	12	15	3	1,2,3	1	1	1
    chr1	15	20	2	1,2	1	1	0
    chr1	20	22	1	2	0	1	0
    chr1	22	30	2	1,2	1	1	0
    chr1	30	32	1	2	0	1	0
    chr1	32	34	1	3	0	0	1


**Example adding a header line**::


    chrom	start	end	num	list	a.bed	b.bed	c.bed
    chr1	6	8	1	1	1	0	0
    chr1	8	12	2	1,3	1	0	1
    chr1	12	15	3	1,2,3	1	1	1
    chr1	15	20	2	1,2	1	1	0
    chr1	20	22	1	2	0	1	0
    chr1	22	30	2	1,2	1	1	0
    chr1	30	32	1	2	0	1	0
    chr1	32	34	1	3	0	0	1


**Example adding a header line and custom file labels**::


    chrom	start	end	num	list	    joe	bob	sue
    chr1	6	8	1	joe	    1	0	0
    chr1	8	12	2	joe,sue	    1	0	1
    chr1	12	15	3	joe,bob,sue 1	1	1
    chr1	15	20	2	joe,bob	    1	1	0
    chr1	20	22	1	bob	    0	1	0
    chr1	22	30	2	joe,bob	    1	1	0
    chr1	30	32	1	bob	    0	1	0
    chr1	32	34	1	sue	    0	0	1


@REFERENCES@

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