--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/hicBuildMatrix.xml	Thu Mar 30 02:30:47 2017 -0400
@@ -0,0 +1,133 @@
+<tool id="hicexplorer_hicbuildmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+    <description>creates a matrix of interactions</description>
+    <macros>
+        <token name="@BINARY@">hicBuildMatrix</token>
+        <import>macros.xml</import>
+    </macros>
+    <expand macro="requirements" >
+        <requirement type="package" version="1.3.1">samtools</requirement>
+    </expand>
+    <command>
+<![CDATA[
+
+        mkdir ./QCfolder &&
+        mkdir $qc.files_path
+        &&
+
+        hicBuildMatrix
+
+            --samFiles
+            #for $repeat in $samFiles:
+                '${repeat.samFile}'
+            #end for
+
+            #if $binSize:
+                --binSize $binSize
+            #end if
+
+            #if $restrictionCutFile:
+                --restrictionCutFile '$restrictionCutFile'
+            #end if
+
+            #if $minDistance:
+                --minDistance $minDistance
+            #end if
+
+            #if $maxDistance:
+                --maxDistance $maxDistance
+            #end if
+
+            #if $restrictionSequence:
+                --restrictionSequence '$restrictionSequence'
+            #end if
+
+            #if $region:
+                --region '$region'
+            #end if
+
+            --outFileName ./matrix.h5
+            --outBam ./unsorted.bam
+
+            #if $restrictionCutFile:
+                --restrictionCutFile '$restrictionCutFile'
+            #end if
+
+            $removeSelfCircles
+
+            #if $minMappingQuality and $minMappingQuality is not None:
+                --minMappingQuality $minMappingQuality
+            #end if
+
+            --QCfolder ./QCfolder
+        &&
+        mv ./QCfolder/* $qc.files_path/
+        &&
+        mv $qc.files_path/hicQC.html $qc
+        &&
+        samtools sort ./unsorted.bam -o sorted.bam
+
+]]>
+    </command>
+    <inputs>
+        <repeat max="2" min="2" name="samFiles" title="Sam/Bam files to process">
+            <param name="samFile" type="data" format="sam,bam"/>
+        </repeat>
+
+        <param argument="--restrictionCutFile" type="data" format="bed" optional="True"
+            help="BED file with all restriction cut places. Should contain only mappable restriction sites. If given, the
+                  bins are set to match the restriction fragments (i.e. the region between one restriction site and the next)"/>
+
+        <param name="binSize" type="integer" value="" optional="true" label="Bin size in bp"
+            help="If used, the restriction cut places (if given) are used to only consider reads that are in the vicinity of the resctriction sites.
+            Otherwise all reads in the interval are considered. " argument="--binSize"/>
+        
+        <param name="restrictionCutFile" type="data" format="bed" optional="true" label="BED file with all restriction cut places"
+            help="Should contaion only  mappable restriction sites. If given, the bins are set to match the restriction fragments
+            (i.e. the region between one restriction site and the next)." argument="--restrictionCutFile"/>
+
+        <param name="minDistance" type="integer" value="" optional="true" label="Minimum distance between restriction sites"
+            help="Restriction sites that are closer that this distance are merged into one.
+            This option only applies if --restrictionCutFile is given." argument="--minDistance"/>
+
+        <param name="maxDistance" type="integer" value="" optional="true" label="Maximum distance in bp from restriction site to read, to consider a read a valid one"
+            help="This option only applies if --restrictionCutFile is given."  argument="--maxDistance"/>
+
+        <param name="restrictionSequence" type="text" optional="true" label="Sequence of the restriction site"
+            help="This is used to discard reads that end/start with such sequence and that are considered un-ligated fragments or
+            &quot;dangling-ends&quot;. If not given, such statistics will not be available." argument="--restrictionSequence"/>
+
+        <expand macro="region" />
+
+        <param argument="--removeSelfCircles" type="boolean" truevalue="--removeSelfCircles" falsevalue=""
+            label="Save the matrix of values underlying the heatmap" help="If set, outward facing reads, at a distance of less thatn 25kbs are removed." />
+
+        <expand macro="minMappingQuality" />
+
+    </inputs>
+    <outputs>
+        <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
+        <data name="outFileName" from_work_dir="matrix.h5" format="h5" label="${tool.name} MATRIX on ${on_string}"/>
+        <data name="qc" format="html" label="${tool.name} QC"/>
+    </outputs>
+    <tests>
+        <test>
+            <repeat name="samFiles">
+                <param name="samFile" value="small_test_R1_unsorted.bam" ftype="sam" />
+            </repeat>
+            <repeat name="samFiles">
+                <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/>
+            </repeat>
+            <param name="binSize" value="5000"/>
+            <output name="outBam" file="hicBuildMatrix_result1.bam" ftype="bam"/>
+            <output name="outFileName" file="hicBuildMatrix_result1.h5" ftype="h5" compare="sim_size"/>
+        </test>
+    </tests>
+    <help><![CDATA[
+
+**What it does**
+
+Creates a matrix of interactions.
+
+]]></help>
+    <expand macro="citations" />
+</tool>