Mercurial > repos > iuc > mothur_shhh_seqs
diff shhh.seqs.xml @ 2:c54bf33450d7 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3
| author | iuc |
|---|---|
| date | Tue, 20 Mar 2018 22:17:05 -0400 |
| parents | fddd81ee5cd4 |
| children | 6ee54b761c3c |
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--- a/shhh.seqs.xml Tue Sep 05 17:19:05 2017 -0400 +++ b/shhh.seqs.xml Tue Mar 20 22:17:05 2018 -0400 @@ -7,31 +7,32 @@ <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=""/> <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/> <param name="group" type="data" format="mothur.groups" optional="true" label="group - Sequences Name reference"/> <param name="sigma" type="float" value=".01" min="0.0" max="1.0" label="sigma" help="default .01"/> + <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -46,11 +47,11 @@ <output name="shhh_fasta" md5="0169152fa33b588cabf3c3b932cc6018" ftype="mothur.align"/> <output name="shhh_names" md5="f3bc939b899d91f7cf3b822c5a822805" ftype="mothur.names"/> <output name="shhh_map" md5="0bcfe53ec754878ca5f6a126114671e1" ftype="txt"/> + <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -60,7 +61,6 @@ .. _shhh.seqs: https://www.mothur.org/wiki/Shhh.seqs -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>