diff hicMergeMatrixBins.xml @ 13:4d8f5bb39a78 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit fa19d3b6a9d0160a13f8d1e4a99f20c4dbe937b2"

--- a/hicMergeMatrixBins.xml	Mon Dec 16 13:21:31 2019 +0000
+++ b/hicMergeMatrixBins.xml	Mon Dec 16 22:46:46 2019 +0000
@@ -6,12 +6,13 @@
     </macros>
     <expand macro="requirements" />
     <command detect_errors="exit_code"><![CDATA[
-        hicMergeMatrixBins
-            --matrix '$matrix_h5_cooler'
+        ln -s '$matrix_h5_cooler' 'matrix.$matrix_h5_cooler.ext' &&
+        @BINARY@
+            --matrix 'matrix.$matrix_h5_cooler.ext'
             --numBins $numBins
             $runningWindow
-            --outFileName matrix.$outputFormat
-        && mv matrix.$outputFormat matrix
+            --outFileName 'matrix.$matrix_h5_cooler.ext'
+        && mv 'matrix.$matrix_h5_cooler.ext' matrix
 
 ]]>
     </command>
@@ -20,15 +21,11 @@
 
         <param argument="--numBins" type="integer" min="1" value="3" label="Number of bins to merge" />
         <param argument="--runningWindow" type="boolean" falsevalue="" truevalue="--runningWindow" label="Set to merge for using a running window of length --numBins. Usually not set." />
-        <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="matrix" format="h5">
+        <data name="outFileName" from_work_dir="matrix" format="cool">
               <change_format>
-                <when input="outputFormat" value="cool" format="cool" />
+                <when input_dataset="matrix_h5_cooler" attribute="ext" value="h5" format="h5"/>
             </change_format>
         </data>
     </outputs>
@@ -36,7 +33,11 @@
         <test>
             <param name="matrix_h5_cooler" value="small_test_matrix.h5"/>
             <param name="numBins" value="5" />
-            <output name="outFileName" file="hicMergeMatrixBins_result1.npz.h5" ftype="h5" compare="sim_size" delta="24000" />
+            <output name="outFileName" ftype="h5">
+                <assert_contents>
+                    <has_h5_keys keys='intervals,matrix,nan_bins'/>
+                </assert_contents>
+            </output>
         </test>
     </tests>
     <help><![CDATA[