--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicPlotMatrix.xml	Thu Mar 30 02:12:31 2017 -0400
@@ -0,0 +1,135 @@
+<tool id="hicexplorer_hicplotmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>Plots a HiC matrix heatmap</description>
+    <macros>
+        <token name="@BINARY@">hicPlotMatrix</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+        ln -s '$matrix' input_matrix.h5 &&
+
+        @BINARY@
+
+            --matrix input_matrix.h5
+
+            #if $title and $title is not None:
+                --title '$title'
+            #end if
+
+            #if $scoreName and $scoreName is not None:
+                --scoreName '$scoreName'
+            #end if
+
+
+            --outFileName plot.svg
+
+            $perChromosome
+            $clearMaskedBins
+
+            --whatToShow $whatToShow.whatToShow_select
+
+
+            ## special: --chromosomeOrder is optional, but if given needs at least one argument
+            #set chroms = '" "'.join([ str($var.chromosome) for $var in $chromosomeOrder ])
+            #if chroms
+                --chromosomeOrder '$chroms'
+            #end if
+
+            #if $region:
+                --region '$region'
+            #end if
+
+            #if $region2:
+                --region2 '$region2'
+            #end if
+            $log1p
+            $log
+
+            #if $colormap:
+                --colorMap $colormap
+            #end if
+
+            #if $vMin:
+                --vMin $vMin
+            #end if
+
+            #if $vMax:
+                --vMax $vMax
+            #end if
+
+            #if $whatToShow.whatToShow_select != 'heatmap':
+                #if $whatToShow.zMax:
+                    --zMax $whatToShow.zMax
+                #end if
+            #end if
+
+]]>
+    </command>
+    <inputs>
+        <param argument="--matrix" type="data" format="h5" label="Hi-C matrix to plot"/>
+        <param argument="--title" type="text" optional="true" label="Plot title"/>
+        <param argument="--scoreName" type="text" optional="true" label="Score name"/>
+        <param argument="--perChromosome" type="boolean" truevalue="--perChromosome" falsevalue="" checked="false"
+            label="Plot per chromosome"
+            help="Instead of plotting the whole matrix each chromosome is plotted next to the other. This parameter is not compatible with --region" />
+        <param argument="--clearMaskedBins" type="boolean" truevalue="--clearMaskedBins" falsevalue="" checked="false"
+            label="Remove masked bins from the matrix"  />
+
+        <conditional name="whatToShow">
+            <param argument="--whatToShow" name="whatToShow_select" type="select" label="Show heatmap/3D">
+                <option value="both">Show both</option>
+                <option value="heatmap" selected="true">Only heatmap</option>
+                <option value="3D">Only 3D</option>
+            </param>
+            <when value="both">
+                <expand macro="zMax" />
+            </when>
+            <when value="3D">
+                <expand macro="zMax" />
+            </when>
+            <when value="heatmap"/>
+        </conditional>
+
+        <repeat name="chromosomeOrder" min="1" title="Chromosomes to include (and order to plot in):"
+            help="This option overrides --region and --region2">
+            <param name="chromosome" type="text" />
+        </repeat>
+
+        <param argument="--region" type="text" optional="True" label="Plot only this region"
+            help="The format is chr:start-end The plotted region contains the main diagonal and is symmetric unless  --region2 is given"/>
+        <param argument="--region2" type="text" optional="True" label="Region two to plot"
+            help="If given then only the region defined by --region and --region2 is plotted. The format is the same as --region"/>
+        <param argument="--log1p" type="boolean" truevalue="--log1p" falsevalue="" checked="false" label="Plot the log1p of the matrix values."/>
+        <param argument="--log" type="boolean" truevalue="--log" falsevalue="" checked="false" label="Plot the *MINUS* log of the matrix values."/>
+
+        <expand macro="colormap" />
+
+        <param argument="--vMin" type="float" optional="true" label="vMin"/>
+        <param argument="--vMax" type="float" optional="true" label="vMax"/>
+
+    </inputs>
+    <outputs>
+        <data name="outFileName" from_work_dir="plot.svg" format="svg" label="${tool.name} on ${on_string}"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="matrix" ftype="h5" value="Li_et_al_2015.h5"/>
+            <param name="region" value="chrX:3000000-3500000"/>
+            <param name="region2" value="chrX:3100000-3600000"/>
+            <param name="log1p" value="True"/>
+            <param name="clearMaskedBins" value="True"/>
+            <param name="whatToShow_select" value="heatmap"/>
+            <output name="outFileName" file="hicPlotMatrix_result1.svg" ftype="svg" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Plots a HiC matrix heatmap.
+
+]]></help>
+    <expand macro="citations" />
+</tool>
+