--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicCorrelate.xml	Thu Mar 30 02:50:08 2017 -0400
@@ -0,0 +1,94 @@
+<tool id="hicexplorer_hiccorrelate" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>Computes pairwise correlations between hic matrices data</description>
+    <macros>
+        <token name="@BINARY@">hicCorrelate</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" />
+    <command>
+<![CDATA[
+
+        @multiple_input_matrices@
+        hicCorrelate
+
+            --matrices $matrices
+            --labels $mlabels
+
+            #if $method and $method is not None:
+                --method $method
+            #end if
+            $log1p
+
+            #if $use_range.select_use_range == "yes_use_range"
+                --range $range_min:$range_max
+            #end if
+
+            #if $chromosomes:
+                --chromosomes #echo '" "'.join([ '"%s"' % $chrom for $chrom in $chromosomes ])#
+            #end if
+
+            --colorMap $colormap
+
+            --outFileNameHeatmap ./heatmap.png
+            --outFileNameScatter ./scatter.png
+]]>
+    </command>
+    <inputs>
+        <expand macro="multiple_input_matrices" />
+
+        <param name="method" type="select" label="Correlation method to use" argument="--method" >
+            <option value="spearman">Spearman</option>
+            <option selected="true" value="pearson">Pearson</option>
+        </param>
+        <param name="log1p" type="boolean" argument="--log1p"  truevalue="--log1p" falsevalue=""
+            label="Use the log1p of the matrix values" help="(--log1p)" />
+        <conditional name="use_range"> <!-- argparse specifies one argument of type min_range:max_range -->
+            <param name="select_use_range" type="select" label="Range restriction (in bp)" argument="--range">
+                <option value="no_use_range">No restriction</option>
+                <option value="yes_use_range">Only consider counts within a range</option>
+            </param>
+            <when value="no_use_range"/>
+            <when value="yes_use_range">
+                <param name="range_min" type="integer" value="" min="0"/>
+                <param name="range_max" type="integer" value="" min="0"/>
+            </when>
+        </conditional>
+        <repeat name="chromosomes" title="List of chromosomes to be included in the correlation" min="0">
+            <param name="chromosome" type="text"/>
+        </repeat>
+
+        <expand macro="colormap" />
+
+    </inputs>
+    <outputs> <!-- not sure if argument is specifiable for output yet, would be cool if so -->
+        <data name="outFileNameHeatmap" from_work_dir="heatmap.png" format="png" />
+        <data name="outFileNameScatter" from_work_dir="scatter.png" format="png" />
+    </outputs>
+    <tests>
+        <test>
+            <repeat name="input_files">
+                <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5"/>
+                <param name="mlabel" value="first"/>
+            </repeat>
+            <repeat name="input_files">
+                <param name="matrix" value="hicCorrectMatrix_result1.npz.h5" ftype="h5" />
+                <param name="mlabel" value="second"/>
+            </repeat>
+            <param name="log1p" value="True"/>
+            <param name="colormap" value="jet"/>
+            <param name="method" value="spearman"/>
+            <output name="outFileNameHeatmap" file="hicCorrelate_heatmap_result1.png" ftype="png" compare="sim_size"/>
+            <output name="outFileNameScatter" file="hicCorrelate_scatter_result1.png" ftype="png" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Computes pairwise correlations between hic matrices data.
+The correlation is computed taking the values from each pair of matrices and discarding values that are zero in both matrices.
+
+
+]]></help>
+    <expand macro="citations" />
+</tool>