diff computeMatrix.xml @ 12:babca70c3586 draft

planemo upload for repository https://github.com/fidelram/deepTools/tree/master/galaxy/wrapper/ commit 09975f870c75347fba5c6777c9f3b442bdeeb289

--- a/computeMatrix.xml	Tue Jan 24 04:59:41 2017 -0500
+++ b/computeMatrix.xml	Fri Mar 31 09:28:45 2017 -0400
@@ -7,17 +7,20 @@
     <expand macro="requirements" />
     <command>
 <![CDATA[
+        #import re
         #import tempfile
         #set bw_files=[]
-        #for $counter, $bigwig in enumerate($scoreFileName):
-            ln -s "${bigwig}" "file_${counter}.bw" &&
-            #silent $bw_files.append('file_%s.bw' % $counter)
+        #for $counter, $bigwig, in enumerate($scoreFileName):
+            #set identifier = re.sub('[^\s\w\-]', '_', str($bigwig.element_identifier))
+            ln -f -s "${bigwig}" "${identifier}_${counter}.bw" &&
+            #silent $bw_files.append('%s_%s.bw' % ($identifier, $counter))
         #end for
 
         #set bed_files=[]
-        #for $counter, $rf in enumerate($regionsFiles):
-            ln -s "${rf.regionsFile}" "group_${counter}.bed" &&
-            #silent $bed_files.append('group_%s.bed' % $counter)
+        #for $counter, $rf, in enumerate($regionsFiles):
+            #set identifier = re.sub('[^\s\w\-]', '_', str($rf.regionsFile.element_identifier))
+            ln -f -s "${rf.regionsFile}" "${identifier}_${counter}.bed" &&
+            #silent $bed_files.append('%s_%s.bed' % ($identifier, $counter))
         #end for
 
         @BINARY@