diff hicSumMatrices.xml @ 7:e0df60f3b0d5 draft

planemo upload for repository https://github.com/maxplanck-ie/HiCExplorer/tree/master/galaxy/wrapper/ commit d76f2040a05a5f8752cbfe9a8bc1ef9efae45c01

--- a/hicSumMatrices.xml	Tue Jan 02 10:18:36 2018 -0500
+++ b/hicSumMatrices.xml	Wed Jan 03 13:31:47 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hicsummatrices" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hicsummatrices" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>combines Hi-C matrices of the same size</description>
     <macros>
         <token name="@BINARY@">hicSumMatrices</token>
@@ -14,11 +14,9 @@
 
         hicSumMatrices
             --matrices "$m"
-        #if $outputFormat == 'h5'
-            --outFileName matrix.h5
-        #elif $outputFormat == 'cool'
-            --outFileName matrix.cool
-        #end if
+            --outFileName matrix.$outputFormat
+        
+        && mv matrix.$outputFormat matrix
 ]]>
     </command>
     <inputs>
@@ -30,11 +28,10 @@
         </param>
     </inputs>
     <outputs>
-        <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5">
-            <filter>outputFormat == 'h5'</filter>
-        </data>
-        <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool">
-            <filter>outputFormat == 'cool'</filter>
+        <data name="outFileName" from_work_dir="matrix" format="h5">
+             <change_format>
+                <when input="outputFormat" value="cool" format="cool" />
+            </change_format>
         </data>
     </outputs>
     <tests>
@@ -42,7 +39,7 @@
             <param name="matrix_h5_cooler_multiple" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/>
             <!-- <param name="matrices" value="hicCorrectMatrix_result1.npz.h5,hicCorrectMatrix_result1.npz.h5"/> -->
             <param name='outputFormat' value='h5'/>
-            <output name="outFileName_h5" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/>
+            <output name="outFileName" file="hicSumMatrices_result1.npz.h5" ftype="h5" compare="sim_size" delta="70000"/>
         </test>
     </tests>
     <help><![CDATA[