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modified bedtools

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File tools/bedtools/bamToBed.xml

+<tool id="bedtools_bamtobed" name="Convert from BAM to BED" version="0.1.0">
+
+<description>
+</description>    
+
+<requirements>
+    <requirement type="binary">bamToBed</requirement>
+</requirements>
+
+<command>
+    bamToBed $option $ed_score -i '$input' &gt; '$output' 
+    #if str($tag):
+      -tag      $tag
+    #end if
+</command>
+
+<inputs>
+    <param format="bam" name="input" type="data" label="Convert the following BAM file to BED"/>
+    <param name="option" type="select" label="What type of BED output would you like">
+        <option value="">Create a 6-column BED file.</option>
+        <option value="-bed12">Create a full, 12-column "blocked" BED file.</option>
+        <option value="-bedpe">Create a paired-end, BEDPE format.</option>
+    </param>
+    <param name="split" type="boolean" label="Report spliced BAM alignments as separate BED entries" truevalue="-split" falsevalue="" checked="false"/>
+    <param name="ed_score" type="boolean" label="Use alignment's edit-distance for BED score" truevalue="-ed" falsevalue="" checked="false"/>
+    <param name="tag" type="text" optional="true" label="Use other NUMERIC BAM alignment tag as the BED score"/>
+</inputs>
+
+<outputs>
+    <data format="bed" name="output" metadata_source="input" label="${input.name} (as BED)"/>
+</outputs>
+
+<help>
+
+**What it does**
+
+This tool converts a BAM file to a BED file. The end coordinate is computed
+by inspecting the CIGAR string. The QNAME for the alignment is used as the 
+BED name field and, by default, the MAPQ is used as the BED score. 
+
+.. class:: infomark
+
+The "Report spliced BAM alignment..." option breaks BAM alignments with the "N" (splice) operator into distinct BED entries.  For example, using this option on a CIGAR such as 50M1000N50M would, by default, produce a single BED record that spans 1100bp.  However, using this option, it would create two separate BED records that are each 50bp in size and are separated by 1000bp (the size of the N operation).  This is important for RNA-seq and structural variation experiments.
+
+
+.. class:: warningmark
+
+If using a custom BAM alignment TAG as  the BED score, note that this must be a numeric tag (e.g., type "i" as in NM:i:0).
+
+.. class:: warningmark
+
+If creating a BEDPE output (see output formatting options), the BAM file should be sorted by query name.
+
+.. class:: warningmark
+
+This tool requires that `bedtools`__ has been installed on your system.
+
+------
+
+This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
+
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://cphg.virginia.edu/quinlan/
+    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
+
+
+
+</help>
+</tool>

File tools/bedtools/coverageBed_counts.xml

+<tool id="bedtools_coveragebed_counts" name="Count intervals in one file overlapping intervals in another file" version="0.1.0">
+
+<description>
+</description>
+
+<requirements>
+    <requirement type="binary">coverageBed</requirement>
+</requirements>
+
+<command>
+    coverageBed
+    #if $inputA.ext == "bam"
+        -abam '$inputA'
+    #else
+        -a '$inputA'
+    #end if
+    -b '$inputB'
+    -counts
+    $split
+    $strand
+    | sort -k1,1 -k2,2n
+    &gt; '$output'
+</command>
+
+<inputs>
+    <param format="bed,bam" name="inputA" type="data" label="Count how many intervals in this BED or BAM file (source)">
+          <validator type="unspecified_build" />
+    </param>
+    <param format="bed" name="inputB" type="data" label="overlap the intervals in this BED file (target)">
+          <validator type="unspecified_build" />
+    </param>
+    <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
+    
+    <param name="strand" type="select" label="Count">
+        <option value="">overlaps on either strand</option>
+        <option value="-s">only overlaps occurring on the **same** strand.</option>
+        <option value="-S">only overlaps occurring on the **opposite** strand.</option>
+    </param>
+</inputs>
+
+<outputs>
+    <data format="bed" name="output" metadata_source="inputB" label="count of overlaps in ${inputA.name} on ${inputB.name}"/>
+</outputs>
+
+<help>
+
+**What it does**
+
+This tool converts counts the number of intervals in a BAM or BED file (the source) that overlap another BED file (the target).
+
+.. class:: infomark
+
+The output file will be comprised of each interval from your original target BED file, plus an additional column indicating the number of intervals in your source file that overlapped that target interval.
+
+.. class:: warningmark
+
+This tool requires that `bedtools`__ has been installed on your system.
+
+------
+
+This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
+
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://cphg.virginia.edu/quinlan/
+    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
+
+</help>
+</tool>

File tools/bedtools/genomeCoverageBed_bedgraph.xml

+<tool id="bedtools_genomecoveragebed_bedgraph" name="Create a BedGraph of genome coverage" version="0.1.0">
+
+    <description>
+    </description>
+    
+    <requirements>
+        <requirement type="binary">genomeCoverageBed</requirement>
+    </requirements>
+
+    <command>genomeCoverageBed
+        #if $input.ext == "bam"
+            -ibam '$input'
+        #else
+            -i '$input'
+            -g ${chromInfo}
+        #end if
+        
+        #if str($scale):
+          -scale      $scale
+        #end if
+        
+        -bg
+        $zero_regions
+        $split
+        $strand
+        &gt; '$output'
+    </command>
+
+    <inputs>
+        <param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed">
+              <validator type="unspecified_build" />
+        </param>
+
+        <param name="zero_regions" type="boolean" checked="true" truevalue="-bga" falsevalue="" label="Report regions with zero coverage" help="If set, regions without any coverage will also be reported." />
+
+        <param name="split" type="boolean" checked="false" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
+
+        <param name="strand" type="select" label="Calculate coverage based on">
+            <option value="">both strands combined</option>
+            <option value="-strand +">positive strand only</option>
+            <option value="-strand -">negative strand only</option>
+        </param>
+
+        <param name="scale" type="text" optional="true" label="Scale the coverage by a constant factor" help="Each BEDGRAPH coverage value is multiplied by this factor before being reported. Useful for normalizing coverage by, e.g., reads per million (RPM)"/>
+    </inputs>
+
+    <outputs>
+        <data format="bedgraph" name="output"  metadata_source="input" label="${input.name} (Genome Coverage BedGraph)" />
+    </outputs>
+    <help>
+
+
+**What it does**
+
+This tool calculates the genome-wide coverage of intervals defined in a BAM or BED file and reports them in BedGraph format.
+
+.. class:: warningmark
+
+The input BED or BAM file must be sorted by chromosome name (but doesn't necessarily have to be sorted by start position).
+
+.. class:: warningmark
+
+This tool requires that `bedtools`__ has been installed on your system.
+
+-----
+
+**Example 1**
+
+Input (BED format)-
+Overlapping, un-sorted intervals::
+
+    chr1    140 176
+    chr1    100 130
+    chr1    120 147
+
+
+Output (BedGraph format)-
+Sorted, non-overlapping intervals, with coverage value on the 4th column::
+
+    chr1    100 120 1
+    chr1    120 130 2
+    chr1    130 140 1
+    chr1    140 147 2
+    chr1    147 176 1
+
+-----
+
+**Example 2 - with ZERO-Regions selected (assuming hg19)**
+
+Input (BED format)-
+Overlapping, un-sorted intervals::
+
+    chr1    140 176
+    chr1    100 130
+    chr1    120 147
+
+
+Output (BedGraph format)-
+Sorted, non-overlapping intervals, with coverage value on the 4th column::
+
+    chr1    0 100 0
+    chr1    100 120 1
+    chr1    120 130 2
+    chr1    130 140 1
+    chr1    140 147 2
+    chr1    147 176 1
+    chr1    176 249250621 0
+
+
+This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
+
+        .. __: http://code.google.com/p/bedtools/
+        .. __: http://code.google.com/p/bedtools/
+        .. __: http://cphg.virginia.edu/quinlan/
+        .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
+</help>
+</tool>

File tools/bedtools/genomeCoverageBed_histogram.xml

+<tool id="bedtools_genomecoveragebed_histogram" name="Create a histogram of genome coverage" version="0.1.0">
+	<description>
+	</description>
+	
+	<requirements>
+        <requirement type="binary">genomeCoverageBed</requirement>
+    </requirements>
+    
+	<command>genomeCoverageBed
+        #if $input.ext == "bam"
+            -ibam '$input'
+        #else
+            -i '$input'
+            -g ${chromInfo}
+        #end if
+		#if str($max):
+          -max      $max
+        #end if
+		&gt; '$output'
+	</command>
+
+	<inputs>
+		<param format="bed,bam" name="input" type="data" label="The BAM or BED file from which coverage should be computed"></param>
+		<param name="max" type="text" optional="true" label="Max depth" help="Combine all positions with a depth >= max into a single bin in the histogram."/>
+	</inputs>
+
+	<outputs>
+		<data format="tabular" name="output"  metadata_source="input" label="${input.name} (Genome Coverage Histogram)" />
+	</outputs>
+
+<help>
+**What it does**
+
+This tool calculates a histogram of genome coverage depth based on mapped reads in BAM format or intervals in BED format.
+
+
+------
+
+.. class:: warningmark
+
+This tool requires that `bedtools`__ has been installed on your system.
+
+.. class:: infomark
+
+The output file will contain five columns:
+
+    * 1. Chromosome name (or 'genome' for whole-genome coverage)
+    * 2. Coverage depth
+    * 3. The number of bases on chromosome (or genome) with depth equal to column 2.
+    * 4. The size of chromosome (or entire genome) in base pairs
+    * 5. The fraction of bases on chromosome (or entire genome) with depth equal to column 2.
+
+**Example Output**::
+    
+    chr2L       0           1379895     23011544    0.0599653
+    chr2L       1           837250      23011544    0.0363839
+    chr2L       2           904442      23011544    0.0393038
+    chr2L       3           913723      23011544    0.0397072
+    chr2L       4           952166      23011544    0.0413778
+    chr2L       5           967763      23011544    0.0420555
+    chr2L       6           986331      23011544    0.0428624
+    chr2L       7           998244      23011544    0.0433801
+    chr2L       8           995791      23011544    0.0432735
+    chr2L       9           996398      23011544    0.0432999
+
+
+
+
+------
+
+This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
+
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://cphg.virginia.edu/quinlan/
+    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
+
+
+
+</help>
+</tool>

File tools/bedtools/intersectBed_bam.xml

+<tool id="bedtools_intersectbed_bam" name="Intersect BAM alignments with intervals in another files" version="0.1.0">
+<description>
+</description>
+    
+<requirements>
+    <requirement type="binary">intersectBed</requirement>
+</requirements>
+
+<command>
+    intersectBed
+    -abam '$inputA'
+    -b '$inputB'
+    $split
+    $strand
+    #if str($fraction):
+      -f      $fraction
+    #end if
+    $reciprocal
+    $invert
+    &gt; '$output'
+</command>
+
+<inputs>
+    <param format="bam" name="inputA" type="data" label="Which alignments in this BAM file">
+          <validator type="unspecified_build" />
+    </param>
+    <param format="bed" name="inputB" type="data" label="overlap intervals in this BED file?">
+          <validator type="unspecified_build" />
+    </param>
+    <param name="split" type="boolean" checked="true" truevalue="-split" falsevalue="" label="Treat split/spliced BAM or BED12 entries as distinct BED intervals when computing coverage." help="If set, the coverage will be calculated based the spliced intervals only. For BAM files, this inspects the CIGAR N operation to infer the blocks for computing coverage. For BED12 files, this inspects the BlockCount, BlockStarts, and BlockEnds fields (i.e., columns 10,11,12). If this option is not set, coverage will be calculated based on the interval's START/END coordinates, and would include introns in the case of RNAseq data." />
+    
+    <param name="strand" type="select" label="Calculate coverage based on">
+        <option value="">Overlaps on either strand</option>
+        <option value="-s">Only overlaps occurring on the **same** strand.</option>
+        <option value="-S">Only overlaps occurring on the **opposite** strand.</option>
+    </param>
+    
+    <param name="fraction" type="text" optional="true" label="Minimum overlap required as a fraction of the BAM alignment" help="Alignments are only retained if the overlap with the an interval in the BED file comprises at least this fraction of the BAM alignment's length.  For example, to require that the overlap affects 50% of the BAM alignment, use 0.50"/>
+    
+    <param name="reciprocal" type="boolean" checked="false" truevalue="-r" falsevalue="" label="Require reciprocal overlap." help="If set, the overlap between the BAM alignment and the BED interval must affect the above fraction of both the alignment and the BED interval." />
+    
+    <param name="invert" type="boolean" checked="false" truevalue="-v" falsevalue="" label="Report only those alignments that **do not** overlap the BED file."/>
+    
+</inputs>
+
+<outputs>
+    <data format="bam" name="output" metadata_source="inputA" label="Intersection of ${inputA.name} and ${inputB.name}"/>
+</outputs>
+
+<help>
+
+**What it does**
+
+This tool creates a new BAM alignment file based on alignments that overlap (or optionally, those that do not overlap) intervals in another BED file.  Example usage would be to cull a BAM file from an exome capture experiment to include on the "on-target" alignments. 
+
+.. class:: infomark
+
+Note that each BAM alignment is treated individually.  Therefore, if one end of a paired-end alignment overlaps an interval in the BED file, yet the other end does not, the output file will only include the overlapping end.
+
+.. class:: infomark
+
+Note that a BAM alignment will be sent to the output file **once** even if it overlaps more than one interval in the BED file.
+
+.. class:: warningmark
+
+This tool requires that `bedtools`__ has been installed on your system.
+
+------
+
+This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
+
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://cphg.virginia.edu/quinlan/
+    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
+
+</help>
+</tool>

File tools/bedtools/multiIntersectBed.xml

+<tool id="bedtools_multiintersectbed" name="Intersect multiple sorted BED files" version="0.1.0">
+	<description>
+	</description>
+	
+	<requirements>
+        <requirement type="binary">multiIntersectBed</requirement>
+    </requirements>
+    
+	<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:: warningmark
+
+This tool requires that `bedtools`__ has been installed on your system.
+
+.. 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
+
+
+-----
+
+
+This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
+
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://cphg.virginia.edu/quinlan/
+    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
+
+
+
+ 
+</help>
+</tool>

File tools/bedtools/unionBedGraphs.xml

+<tool id="bedtools_mergebedgraph" name="Merge BedGraph files" version="0.1.0">
+	<description>
+	</description>
+	
+	<requirements>
+        <requirement type="binary">unionBedGraphs</requirement>
+    </requirements>
+    
+	<command>unionBedGraphs
+		$header
+		-filler '$filler'
+		#if $zero.value == True:
+			-empty
+			-g ${chromInfo}
+		#end if
+		
+		-i '$input1'
+		'$input2'
+		#for $q in $bedgraphs
+			'${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 $bedgraphs
+			#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="bedgraph" type="data" label="First BedGraph 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="bedgraph" type="data" label="Second BedGraph 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="bedgraphs" title="Add'l BedGraph files" >
+			<param name="input" format="bedgraph" type="data" label="BedGraph 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 with zero coverage" help="If set, regions without any coverage will also be reported. Requires a valid organism key for all input datasets" />
+
+		<param name="filler" type="text" value="0" label="Text to use for no-coverage value" help="Can be 0.0, N/A, - or any other value." />
+	</inputs>
+
+	<outputs>
+		<data format="tabular" name="output"  metadata_source="input1" label="Merged BedGraphs of ${input1.name}, ${input2.name} and so on." />
+	</outputs>
+	<help>
+	
+**What it does**
+
+This tool merges multiple BedGraph files, allowing direct and fine-scale coverage comparisons among many samples/files. The BedGraph files need not represent the same intervals; the tool will identify both common and file-specific intervals. In addition, the BedGraph values need not be numeric: one can use any text as the BedGraph value and the tool will compare the values from multiple files.
+
+.. image:: http://people.virginia.edu/~arq5x/files/bedtools-galaxy/ubg.png
+
+
+.. class:: warningmark
+
+This tool requires that each BedGraph file is reference-sorted (chrom, then start) and contains non-overlapping intervals (within a given file).
+
+.. class:: warningmark
+
+This tool requires that `bedtools`__ has been installed on your system.
+
+------
+
+**Example input**::
+
+    # 1.bedgraph
+    chr1  1000    1500    10
+    chr1  2000    2100    20
+
+    # 2.bedgraph
+    chr1  900       1600    60
+    chr1  1700    2050    50
+
+    # 3.bedgraph
+    chr1  1980    2070    80
+    chr1  2090    2100    20
+
+
+------
+
+**Examples using the Zero Coverage checkbox**
+
+Output example (*without* checking "Report regions with zero coverage")::
+    
+    chr1     900    1000     0    60     0
+    chr1    1000    1500    10    60     0
+    chr1    1500    1600     0    60     0
+    chr1    1700    1980     0    50     0
+    chr1    1980    2000     0    50    80
+    chr1    2000    2050    20    50    80
+    chr1    2050    2070    20     0    80
+    chr1    2070    2090    20     0     0
+    chr1    2090    2100    20     0    20
+
+
+Output example (*with* checking "Report regions with zero coverage"). The lines marked with (*) are not covered in any input file, but are still reported (The asterisk marking does not appear in the file).::
+    
+    chr1       0          900     0     0     0 (*)
+    chr1     900         1000     0    60     0
+    chr1    1000         1500    10    60     0
+    chr1    1500         1600     0    60     0
+    chr1    1600         1700     0     0     0 (*)
+    chr1    1700         1980     0    50     0
+    chr1    1980         2000     0    50    80
+    chr1    2000         2050    20    50    80
+    chr1    2050         2070    20     0    80
+    chr1    2070         2090    20     0     0
+    chr1    2090         2100    20     0    20
+    chr1    2100    247249719     0     0     0 (*) 
+
+
+------
+
+**Examples adjusting the "Filler value" for no-covered intervals**
+
+The default value is '0', but you can use any other value.
+
+Output example with **filler = N/A**::
+    
+    chr1     900    1000    N/A     60    N/A
+    chr1    1000    1500     10     60    N/A
+    chr1    1500    1600    N/A     60    N/A
+    chr1    1600    1700    N/A    N/A    N/A
+    chr1    1700    1980    N/A     50    N/A
+    chr1    1980    2000    N/A     50     80
+    chr1    2000    2050     20     50     80
+    chr1    2050    2070     20    N/A     80
+    chr1    2070    2090     20    N/A    N/A
+    chr1    2090    2100     20    N/A     20
+
+
+------
+
+**Examples using the "sample name" labels**::
+
+    chrom   start   end     WT-1    WT-2    KO-1
+    chr1    900     1000    N/A     60      N/A
+    chr1    1000    1500     10     60      N/A
+    chr1    1500    1600    N/A     60      N/A
+    chr1    1600    1700    N/A    N/A      N/A
+    chr1    1700    1980    N/A     50      N/A
+    chr1    1980    2000    N/A     50      80
+    chr1    2000    2050     20     50      80
+    chr1    2050    2070     20    N/A      80
+    chr1    2070    2090     20    N/A      N/A
+    chr1    2090    2100     20    N/A      20
+
+
+------
+
+**Non-numeric values**
+
+The input BedGraph files can contain any kind of value in the fourth column, not necessarily a numeric value.
+
+Input Example::
+        
+    File-1                           File-2 
+    chr1   200   300   Sample1       chr1   100   240   0.75
+    chr1   400   450   Sample1       chr1   250   700   0.43
+    chr1   530   600   Sample2
+
+Output Example::
+    
+    chr1   100    200    0         0.75
+    chr1   200    240    Sample1   0.75
+    chr1   240    250    Sample1   0
+    chr1   250    300    Sample1   0.43
+    chr1   300    400    0         0.43
+    chr1   400    450    Sample1   0.43
+    chr1   450    530    0         0.43
+    chr1   530    600    Sample2   0.43
+    chr1   600    700    0         0.43
+
+
+-----
+
+This tool is part of the `bedtools package`__ from the `Quinlan laboratory`__. If you use this tool, please cite `Quinlan AR, and Hall I.M. BEDTools: A flexible framework for comparing genomic features. Bioinformatics, 2010, 26, 6.`__
+
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://code.google.com/p/bedtools/
+    .. __: http://cphg.virginia.edu/quinlan/
+    .. __: http://bioinformatics.oxfordjournals.org/content/26/6/841.short
+
+
+
+ 
+</help>
+</tool>