# HG changeset patch
# User iuc
# Date 1515003596 18000
# Node ID 1111999ae668de6c4ea3c470ea5841df401c09f1
# Parent  936741507eb10b4ed05980e1a312d016b005e450
planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01

diff -r 936741507eb1 -r 1111999ae668 hicMergeMatrixBins.xml
--- a/hicMergeMatrixBins.xml	Tue Jan 02 09:47:24 2018 -0500
+++ b/hicMergeMatrixBins.xml	Wed Jan 03 13:19:56 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicmergematrixbins" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>Merges bins from a Hi-C matrix</description>
     <macros>
         <token name="@BINARY@">hicMergeMatrixBins</token>
@@ -10,7 +10,8 @@
             --matrix '$matrix_h5_cooler'
             --numBins $numBins
             $runningWindow
-            --outFileName ./out.npz.h5
+            --outFileName matrix.$outputFormat
+        && mv matrix.$outputFormat matrix
 
 ]]>
     </command>
@@ -19,9 +20,17 @@
 
         <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
         <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Merge using a running window of length --numBins" />
+        <param name='outputFormat' type='select' label="Output file format">
+            <option value='h5' selected='true'>HiCExplorer format</option>
+            <option value="cool">cool</option>
+        </param>
     </inputs>
     <outputs>
-        <data name="outFileName" from_work_dir="out.npz.h5" format="h5"/>
+        <data name="outFileName" from_work_dir="matrix" format="h5">
+              <change_format>
+                <when input="outputFormat" value="cool" format="cool" />
+            </change_format>
+        </data>
     </outputs>
     <tests>
         <test>