Mercurial > repos > iuc > mothur_filter_seqs
diff filter.seqs.xml @ 4:e71c69acde3f draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit be5c8af076296a53959fc3ed2b82d92dc7607eeb
author | iuc |
---|---|
date | Mon, 23 Apr 2018 09:34:35 -0400 |
parents | c799faca02a1 |
children |
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--- a/filter.seqs.xml Fri Apr 06 04:06:02 2018 -0400 +++ b/filter.seqs.xml Mon Apr 23 09:34:35 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>