Mercurial > repos > iuc > bbtools_bbmap

diff bbmap.xml @ 3:8157a81f511c draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/bbtools commit 425671870866660485ef6a35c94d3736f5c1df97"
author iuc
date Tue, 01 Feb 2022 23:01:08 +0000
parents e0ca2ec4f5d9
children 6d44c9f1a42b
line wrap: on
line diff
--- a/bbmap.xml	Thu Nov 11 16:38:09 2021 +0000
+++ b/bbmap.xml	Tue Feb 01 23:01:08 2022 +0000
@@ -16,18 +16,16 @@
 
 #if str($input_type_cond.input_type) in ['single', 'pair']:
     #set read1 = $input_type_cond.read1
-    #set read1_identifier = re.sub('[^\s\w\-]', '_', str($read1.element_identifier))
     ## bbmap uses the file extension to determine the input format.
-    #set ext = $read1_identifier + '.fastq'
+    #set ext = '.fastq'
     #if $read1.ext.endswith('.gz'):
         #set ext = $ext + '.gz'
     #end if
-    #set read1_file = $read1_identifier + $ext
+    #set read1_file = 'forward' + $ext
     ln -s '${read1}' '${read1_file}' &&
     #if str($input_type_cond.input_type) == 'pair':
         #set read2 = $input_type_cond.read2
-        #set read2_identifier = re.sub('[^\s\w\-]', '_', str($read2.element_identifier))
-        #set read2_file = $read2_identifier + $ext
+        #set read2_file = 'reverse' + $ext
         ln -s '${read2}' '${read2_file}' &&
     #end if
 #else: