diff picard_NormalizeFasta.xml @ 9:41b8d087a2d2 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/tools/picard commit 74ee0f0b594075fab7f707aaffb4a7f9dac35f2f

--- a/picard_NormalizeFasta.xml	Tue Dec 06 10:04:26 2016 -0500
+++ b/picard_NormalizeFasta.xml	Wed Dec 07 14:56:16 2016 -0500
@@ -8,12 +8,13 @@
     @java_options@
 
     ## Two lines below are due to the fact that picard likes fasta files to have extension .fa
-    ln -s '$inputFile' '$inputFile.element_identifier'.fa &&
-
+    #import re
+    #set escaped_element_identifier = re.sub('[^\w\-]', '_', str($inputFile.element_identifier))
+    ln -f -s '$inputFile' '$escaped_element_identifier'.fa &&
     picard
     NormalizeFasta
 
-    INPUT='$inputFile.element_identifier'.fa
+    INPUT='$escaped_element_identifier'.fa
     OUTPUT="${outFile}"
     LINE_LENGTH="${line_length}"
     TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE="${truncate_sequence_names_at_whitespaces}"