diff filter.seqs.xml @ 7:f93cee78b339 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb

--- a/filter.seqs.xml	Fri Apr 06 03:22:18 2018 -0400
+++ b/filter.seqs.xml	Mon Apr 23 08:53:54 2018 -0400
@@ -8,6 +8,7 @@
     <expand macro="version_command"/>
     <command><![CDATA[
 @SHELL_OPTIONS@
+#import re
 
 ## create symlinks to input datasets
 ln -s '$fasta' fasta.dat &&
@@ -33,9 +34,11 @@
 | tee mothur.out.log &&
 
 ## rename collection files for more transparent element naming
-mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta
+#set $identifier=re.sub('[^\w\-\s\.]', '_', str($fasta.element_identifier))
+mv fasta.filter.fasta '${identifier}.filter.fasta'
 #for i in $inputs:
-    && mv fasta${inputs.index($i)}.filter.fasta "${i.fasta.element_identifier}".filter.fasta
+    #set $identifier=re.sub('[^\w\-\s]', '_', str($i.fasta.element_identifier))
+    && mv fasta${inputs.index($i)}.filter.fasta '${identifier}.filter.fasta'
 #end for
     ]]></command>
     <inputs>