--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/unionBedGraphs.xml	Wed Apr 29 12:06:53 2015 -0400
@@ -0,0 +1,232 @@
+<tool id="bedtools_unionbedgraph" name="Merge BedGraph files" version="@WRAPPER_VERSION@.0">
+    <description></description>
+    <macros>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <expand macro="stdio" />
+    <command>
+<![CDATA[
+    unionBedGraphs
+        $header
+        -filler "${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 $bg in $tag.bedgraphs:
+                "${bg.input}"
+            #end for
+            -names
+            #for $bg in $tag.bedgraphs:
+                "${bg.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="bedgraph" type="data" multiple="True" label="BedGraph files" />
+            </when>
+            <when value="custom">
+                <repeat name="bedgraphs" title="Add BedGraph files" min="2" >
+                    <param name="input" format="bedgraph" type="data" multiple="True" label="BedGraph file" />
+                    <param name="custom_name" type="text" area="false" label="Custom sample name"/>
+                </repeat>
+            </when>
+        </conditional>
+        <expand macro="genome" />
+        <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="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 name="output" format="bedgraph" />
+    </outputs>
+    <tests>
+        <test>
+            <param name="tag_select" value="tag"/>
+            <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
+            <param name="zero" value="False"/>
+            <output name="output" file="unionBedGraphs_result1.bg" ftype="bedgraph" />
+        </test>
+        <test>
+            <param name="tag_select" value="tag"/>
+            <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
+            <param name="header" value="True"/>
+            <param name="zero" value="False"/>
+            <output name="output" file="unionBedGraphs_result2.bg" ftype="bedgraph" />
+        </test>
+        <test>
+            <param name="tag_select" value="tag"/>
+            <param name="inputs" value="unionBedGraphs1.bg,unionBedGraphs2.bg,unionBedGraphs3.bg" ftype="bedgraph" />
+            <param name="zero" value="True"/>
+            <param name="genome" value="unionBedGraphs1.len"/>
+            <output name="output" file="unionBedGraphs_result3.bg" ftype="bedgraph" />
+        </test>
+        <test>
+            <param name="tag_select" value="custom"/>
+            <repeat name="bedgraphs">
+                <param name="input" value="unionBedGraphs1.bg" />
+                <param name="custom_name" value="first" />
+            </repeat>
+            <repeat name="bedgraphs">
+                <param name="input" value="unionBedGraphs2.bg" />
+                <param name="custom_name" value="second" />
+            </repeat>
+            <repeat name="bedgraphs">
+                <param name="input" value="unionBedGraphs3.bg" />
+                <param name="custom_name" value="third" />
+            </repeat>
+            <param name="zero" value="True"/>
+            <param name="genome" value="unionBedGraphs1.len"/>
+            <output name="output" file="unionBedGraphs_result4.bg" ftype="bedgraph" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+**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).
+
+
+------
+
+**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
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>