--- a/hicBuildMatrix.xml	Sun Oct 09 17:35:32 2016 -0400
+++ b/hicBuildMatrix.xml	Wed Mar 29 17:54:01 2017 -0400
@@ -4,10 +4,16 @@
         <token name="@BINARY@">hicBuildMatrix</token>
         <import>macros.xml</import>
     </macros>
-    <expand macro="requirements" />
+    <expand macro="requirements" >
+        <requirement type="package" version="1.3.1">samtools</requirement>
+    </expand>
     <command>
 <![CDATA[
 
+        mkdir ./QCfolder &&
+        mkdir $qc.files_path
+        &&
+
         hicBuildMatrix
 
             --samFiles
@@ -15,35 +21,31 @@
                 '${repeat.samFile}'
             #end for
 
-            #if $binSize and $binSize is not None:
+            #if $binSize:
                 --binSize $binSize
             #end if
 
-            #if $fragmentLength and $fragmentLength is not None:
-                --fragmentLength $fragmentLength
+            #if $restrictionCutFile:
+                --restrictionCutFile '$restrictionCutFile'
             #end if
 
-            #if $restrictionCutFile and $restrictionCutFile is not None:
-                --restrictionCutFile $restrictionCutFile
-            #end if
-
-            #if $minDistance and $minDistance is not None:
+            #if $minDistance:
                 --minDistance $minDistance
             #end if
 
-            #if $maxDistance and $maxDistance is not None:
+            #if $maxDistance:
                 --maxDistance $maxDistance
             #end if
 
-            #if $restrictionSequence and $restrictionSequence is not None:
+            #if $restrictionSequence:
                 --restrictionSequence '$restrictionSequence'
             #end if
 
-            #if $region and $region is not None:
+            #if $region:
                 --region '$region'
             #end if
 
-            --outFileName ./numpy_array.npz
+            --outFileName ./matrix.h5
             --outBam ./unsorted.bam
 
             #if $restrictionCutFile:
@@ -52,11 +54,16 @@
 
             $removeSelfCircles
 
-            #if $minMappingQuality
+            #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
 
 ]]>
@@ -70,21 +77,19 @@
             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="10000" label="Bin size in bp"
+        <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="fragmentLength" type="integer" value="300" optional="true" label="Estimated fragment length" argument="--fragmentLength" />
-
+        
         <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="300" optional="true" label="Minimum distance between restriction sites"
+        <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="800" optional="true" label="Maximum distance in bp from restriction site to read, to consider a read a valid one"
+        <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"
@@ -98,30 +103,30 @@
 
         <expand macro="minMappingQuality" />
 
-
     </inputs>
     <outputs>
         <data name="outBam" from_work_dir="sorted.bam" format="bam" label="${tool.name} BAM file on ${on_string}"/>
-        <data name="outFileName" from_work_dir="numpy_array.npz.h5" format="h5" label="${tool.name} MATRIX 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="r1.sam" ftype="sam" />
+                <param name="samFile" value="small_test_R1_unsorted.bam" ftype="sam" />
             </repeat>
             <repeat name="samFiles">
-                <param name="samFile" value="r2.sam" ftype="sam"/>
+                <param name="samFile" value="small_test_R2_unsorted.bam" ftype="sam"/>
             </repeat>
-            <param name="binSize" value="10000"/>
+            <param name="binSize" value="5000"/>
             <output name="outBam" file="hicBuildMatrix_result1.bam" ftype="bam"/>
-            <output name="outFileName" file="hicBuildMatrix_result1.npz.h5" ftype="h5" compare="sim_size"/>
+            <output name="outFileName" file="hicBuildMatrix_result1.h5" ftype="h5" compare="sim_size"/>
         </test>
     </tests>
     <help><![CDATA[
 
 **What it does**
 
-Creates a matrix of interactions
+Creates a matrix of interactions.
 
 ]]></help>
     <expand macro="citations" />