--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicPlotDistVsCounts.xml	Sun Oct 09 17:35:43 2016 -0400
@@ -0,0 +1,70 @@
+<tool id="hicexplorer_hicplotdistvscounts" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>distance vs HiC counts plot per chromosome</description>
+    <macros>
+        <token name="@BINARY@">hicPlotDistVsCounts</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+
+
+        ln -s '$matrix' input_matrix.npz.h5 &&
+
+        @BINARY@
+
+            --matrix input_matrix.npz.h5
+            $skipDiagonal
+            --plotFile plot.png
+            #if $plotTitle and $plotTitle is not None:
+                --plotTitle '$plotTitle'
+            #end if
+
+            ## special: --chromosomeExclude is optional, but if given needs at least one argument
+            #set chroms = '" "'.join([ str($var.chromosomeExclude) for $var in $chromosomeExclude ])
+            #if $chromosomeExclude:
+                --chromosomeExclude $chroms
+            #end if
+
+]]>
+    </command>
+    <inputs>
+        <param argument="--matrix" type="data" format="h5" label="Hi-C normalized/corrected matrix"/>
+
+        <param argument="--skipDiagonal" type="boolean" truevalue="--skipDiagonal" falsevalue="" label="Exclude diagonal counts" />
+        <param argument="--plotTitle" type="text" optional="true" label="Plot title"/>
+        <repeat name="chromosomeExclude" min="0" title="Chromosomes to exclude">
+            <param argument="--chromosomeExclude" type="text" value="" />
+        </repeat>
+
+    </inputs>
+    <outputs>
+        <data name="plotFile" from_work_dir="plot.png" format="png" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" ftype="h5" value="hicCorrectMatrix_result1.npz.h5"/>
+            <param name="skipDiagonal" value="False"/>
+            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
+        </test>
+        <test>
+            <param name="matrix" ftype="h5" value="hicCorrectMatrix_result1.npz.h5"/>
+            <param name="skipDiagonal" value="False"/>
+            <param name="plotTitle" value="Excluded chrUextra"/>
+            <repeat name="chromosomeExclude">
+                <param name="chromosomeExclude" value="chrUextra"/>
+            </repeat>
+            <output name="plotFile" file="hicPlotDistVsCounts_result1.png" ftype="png" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+This program makes a distance vs. hi-c counts plot per chromosome.
+
+
+]]></help>
+    <expand macro="citations" />
+</tool>
+