--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/multiIntersectBed.xml	Tue Nov 04 01:45:04 2014 -0500
@@ -0,0 +1,196 @@
+<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>