<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>