Mercurial > repos > iuc > mothur_filter_seqs

comparison filter.seqs.xml @ 4:e71c69acde3f draft

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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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3:4e091f12ba0e 4:e71c69acde3f
6 <expand macro="requirements"/> 6 <expand macro="requirements"/>
7 <expand macro="stdio"/> 7 <expand macro="stdio"/>
8 <expand macro="version_command"/> 8 <expand macro="version_command"/>
9 <command><![CDATA[ 9 <command><![CDATA[
10 @SHELL_OPTIONS@ 10 @SHELL_OPTIONS@
11 #import re
11 12
12 ## create symlinks to input datasets 13 ## create symlinks to input datasets
13 ln -s '$fasta' fasta.dat && 14 ln -s '$fasta' fasta.dat &&
14 #for $i in $inputs: 15 #for $i in $inputs:
15 ln -s '$i.fasta' fasta${inputs.index($i)}.dat && 16 ln -s '$i.fasta' fasta${inputs.index($i)}.dat &&
31 | sed 's/ //g' ## mothur trips over whitespace 32 | sed 's/ //g' ## mothur trips over whitespace
32 | mothur 33 | mothur
33 | tee mothur.out.log && 34 | tee mothur.out.log &&
34 35
35 ## rename collection files for more transparent element naming 36 ## rename collection files for more transparent element naming
36 mv fasta.filter.fasta "${fasta.element_identifier}".filter.fasta 37 #set $identifier=re.sub('[^\w\-\s\.]', '_', str($fasta.element_identifier))
38 mv fasta.filter.fasta '${identifier}.filter.fasta'
37 #for i in $inputs: 39 #for i in $inputs:
38 && mv fasta${inputs.index($i)}.filter.fasta "${i.fasta.element_identifier}".filter.fasta 40 #set $identifier=re.sub('[^\w\-\s]', '_', str($i.fasta.element_identifier))
41 && mv fasta${inputs.index($i)}.filter.fasta '${identifier}.filter.fasta'
39 #end for 42 #end for
40 ]]></command> 43 ]]></command>
41 <inputs> 44 <inputs>
42 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/> 45 <param name="fasta" type="data" format="mothur.align" label="fasta - Alignment Fasta"/>
43 <repeat name="inputs" title="Additional Alignment File"> 46 <repeat name="inputs" title="Additional Alignment File">