Mercurial > repos > iuc > mothur_shhh_seqs
diff shhh.seqs.xml @ 3:996697eb1f9e draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 10:02:26 -0500 |
| parents | 48c4a9ef85e6 |
| children | 7afaa6a1ab4a |
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--- a/shhh.seqs.xml Tue Sep 05 16:48:38 2017 -0400 +++ b/shhh.seqs.xml Wed Feb 14 10:02:26 2018 -0500 @@ -7,25 +7,25 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$fasta" fasta.dat && - ln -s "$name" name.dat && - ln -s "$group" group.dat && +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +ln -s '$name' name.dat && +ln -s '$group' group.dat && - echo 'shhh.seqs( - fasta=fasta.dat, - name=name.dat, - #if $group: - group=group.dat, - #end if - sigma=$sigma, - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'shhh.seqs( + fasta=fasta.dat, + name=name.dat, + #if $group: + group=group.dat, + #end if + sigma=$sigma, + processors='\${GALAXY_SLOTS:-8}' +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log ]]></command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Sequences" help=""/> @@ -49,8 +49,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -60,7 +59,6 @@ .. _shhh.seqs: https://www.mothur.org/wiki/Shhh.seqs -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>