diff hicCorrectMatrix.xml @ 7:1612e9458940 draft

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

--- a/hicCorrectMatrix.xml	Tue Jan 02 10:17:05 2018 -0500
+++ b/hicCorrectMatrix.xml	Wed Jan 03 13:30:22 2018 -0500
@@ -1,4 +1,4 @@
-<tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.0">
+<tool id="hicexplorer_hiccorrectmatrix" name="@BINARY@" version="@WRAPPER_VERSION@.1">
     <description>Runs Dekker's iterative correction over a hic matrix.</description>
     <macros>
         <token name="@BINARY@">hicCorrectMatrix</token>
@@ -20,11 +20,7 @@
             #if $mode.mode_selector == 'correct':
 
                 --iterNum $mode.iterNum
-                #if $mode.outputFormat == 'h5'
-                    --outFileName matrix.h5
-                #elif $mode.outputFormat == 'cool'
-                    --outFileName matrix.cool
-                #end if
+                --outFileName matrix.$mode.outputFormat
 
                 #if $mode.filterThreshold_low and $mode.filterThreshold_large:
                     --filterThreshold $mode.filterThreshold_low $mode.filterThreshold_large
@@ -60,7 +56,9 @@
                     --xMax $mode.xMax
                 #end if
             #end if
-
+        #if $mode.mode_selector == 'correct':
+            && mv matrix.$mode.outputFormat matrix
+        #end if
 ]]>
     </command>
     <inputs>
@@ -114,16 +112,14 @@
 
     </inputs>
     <outputs>
-        <data name="outFileName_h5" from_work_dir="matrix.h5" format="h5">
-            <filter>outputFormat == 'h5'</filter>
+        <data name="outFileName" from_work_dir="matrix" format="h5">
+            <change_format>
+                <when input="mode.outputFormat" value="cool" format="cool" />
+            </change_format>
             <filter>mode['mode_selector'] == "correct"</filter>
             
         </data>
-        <data name="outFileName_cool" from_work_dir="matrix.cool" format="cool">
-            <filter>outputFormat == 'cool'</filter>
-            <filter>mode['mode_selector'] == "correct"</filter>
-            
-        </data>
+        
        
         <data name="diagnostic_plot" from_work_dir="diagnostic_plot.png" format="png">
             <filter>mode['mode_selector'] == "diagnostic_plot"</filter>