--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/bigwigCompare.xml	Wed Dec 16 16:36:25 2015 -0500
@@ -0,0 +1,139 @@
+<tool id="deeptools_bigwig_compare" name="bigwigCompare" version="@WRAPPER_VERSION@.0">
+    <description>normalizes and compares two bigWig files to obtain the ratio, log2ratio or difference</description>
+    <macros>
+        <token name="@BINARY@">bigwigCompare</token>
+        <import>deepTools_macros.xml</import>
+    </macros>
+    <expand macro="requirements"/>
+    <command>
+<![CDATA[
+        @BINARY@
+            @THREADS@
+            --bigwig1 '$bigwigFile1'
+            --bigwig2 '$bigwigFile2'
+
+            --outFileName '$outFileName'
+            --outFileFormat '$outFileFormat'
+
+            --ratio $comparison.comparison_select
+
+            #if $comparison.comparison_select in ['ratio','log2']:
+                --pseudocount $comparison.pseudocount
+            #end if
+
+            #if str($region).strip() != '':
+                --region '$region'
+            #end if
+
+            #if $advancedOpt.showAdvancedOpt == "yes":
+
+              $advancedOpt.keepNAs
+              --scaleFactors '$advancedOpt.scaleFactor1:$advancedOpt.scaleFactor2'
+              --binSize $advancedOpt.binSize
+
+                #if $advancedOpt.plotTitle and str($advancedOpt.plotTitle.value) != "":
+                    --plotTitle '$advancedOpt.plotTitle'
+                #end if
+
+            #end if
+]]>
+    </command>
+    <inputs>
+        <param name="bigwigFile1" format="bigwig" type="data" label="Treatment bigwig file" />
+        <param name="bigwigFile2" format="bigwig" type="data" label="bigWig file" />
+
+        <conditional name="comparison">
+            <param name="comparison_select" type="select" 
+                label="How to compare the two files"
+                help="The default is to output the log2ratio between the two samples.
+                The reciprocal ratio returns the negative of the inverse of the ratio if
+                the ratio is less than 0. The resulting values are interpreted as negative fold changes. (--ratio)">
+                <option value="log2" selected="true">compute log2 of the number of reads ratio</option>
+                <option value="ratio">compute the ratio of the number of reads</option>
+                <option value="subtract">compute difference (subtract input from treatment) of the number of reads</option>
+                <option value="add">compute the sum over all reads</option>
+                <option value="reciprocal_ratio">Computes the fold change. If the fold change is less than 1, the negative of the inverse is reported. E.g. A fold change of 10 to 5 would be reported not as 0.5 but as -2</option>
+            </param>
+            <when value="log2">
+                <expand macro="pseudocount" />
+            </when>
+            <when value="ratio">
+                <expand macro="pseudocount" />
+            </when>
+            <when value="subtract" />
+            <when value="add" />
+            <when value="reciprocal_ratio">
+                <expand macro="pseudocount" />
+            </when>
+        </conditional>
+
+        <param name="outFileFormat" type="select" label="Coverage file format">
+            <option value="bigwig" selected="true">bigwig</option>
+            <option value="bedgraph">bedgraph</option>
+        </param>
+
+        <expand macro="region_limit_operation" />
+
+        <conditional name="advancedOpt">
+            <param name="showAdvancedOpt" type="select" label="Show advanced options" >
+                <option value="no" selected="true">no</option>
+                <option value="yes">yes</option>
+            </param>
+            <when value="no" />
+            <when value="yes">
+                <param argument="--binSize" type="integer" value="50" min="1" 
+                    label="Length, in base pairs, of the non-overlapping bin for averaging the score over the regions length"
+                    help="Size of the bins in bp for the output of the bigwig/bedgraph file."/>
+
+                <expand macro="keepNAs" />
+                <expand macro="scaleFactor" />
+                <expand macro="plotTitle" />
+            </when>
+        </conditional>
+    </inputs>
+    <outputs>
+        <data format="bigwig" name="outFileName">
+            <change_format>
+                <when input="outFileFormat" value="bigwig" format="bigwig" />
+                <when input="outFileFormat" value="bedgraph" format="bedgraph" />
+            </change_format>
+        </data>
+    </outputs>
+    <tests>
+        <test>
+            <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
+            <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
+            <param name="showAdvancedOpt" value="no" />
+            <param name="outFileFormat" value="bigwig" />
+            <param name="binSize" value="5" />
+            <param name="comparison_select" value="ratio" />
+            <output name="outFileName" file="bigwigCompare_result1.bw" ftype="bigwig" />
+        </test>
+        <test>
+            <param name="bigwigFile1" value="test.bw" ftype="bigwig" />
+            <param name="bigwigFile2" value="test.bw" ftype="bigwig" />
+            <param name="showAdvancedOpt" value="no" />
+            <param name="outFileFormat" value="bedgraph" />
+            <param name="binSize" value="10" />
+            <param name="comparison_select" value="ratio" />
+            <output name="outFileName" file="bigwigCompare_result2.bg" ftype="bedgraph" />
+        </test>
+    </tests>
+    <help>
+<![CDATA[
+
+**What it does**
+
+This tool compares two bigwig files based on the number of mapped reads. To
+compare the bigwig files the genome is partitioned into bins of equal size,
+then the number of reads found in each BAM file are counted for such bins and
+finally a summarizing value is reported. This value can be the ratio of the
+number of reads per bin, the log2 of the ratio, the sum or the difference.
+
+-----
+
+@REFERENCES@
+]]>
+    </help>
+    <expand macro="citations" />
+</tool>