Mercurial > repos > iuc > mothur_degap_seqs

comparison degap.seqs.xml @ 3:de6d0eaca0ed draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
author iuc
date Wed, 14 Feb 2018 09:39:59 -0500
parents 7e334883931c
children 2f615bc86373
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2:2476b5f869d8 3:de6d0eaca0ed
5 </macros> 5 </macros>
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 11
12 ## create symlinks to input datasets 12 ## create symlinks to input datasets
13 ln -s "$fasta" fasta.dat && 13 ln -s '$fasta' fasta.dat &&
14 14
15 echo 'degap.seqs( 15 echo 'degap.seqs(
16 fasta=fasta.dat 16 fasta=fasta.dat
17 )' 17 )'
18 | sed 's/ //g' ## mothur trips over whitespace 18 | sed 's/ //g' ## mothur trips over whitespace
19 | mothur 19 | mothur
20 | tee mothur.out.log 20 | tee mothur.out.log
21 ]]></command> 21 ]]></command>
22 <inputs> 22 <inputs>
23 <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/> 23 <param name="fasta" type="data" format="fasta" label="fasta - Dataset"/>
24 </inputs> 24 </inputs>
25 <outputs> 25 <outputs>