Mercurial > repos > iuc > mothur_trim_flows
diff trim.flows.xml @ 3:5c31047be933 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:30:46 -0500 |
| parents | 054074503e50 |
| children | 40d7b488661e |
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--- a/trim.flows.xml Tue Sep 05 16:09:58 2017 -0400 +++ b/trim.flows.xml Wed Feb 14 09:30:46 2018 -0500 @@ -7,41 +7,42 @@ <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ - @SHELL_OPTIONS@ +@SHELL_OPTIONS@ - ## create symlinks to input datasets - ln -s "$flow" flow.dat && - #if $oligo.add == "yes": - ln -s "$oligo.oligos" oligo.oligos.dat && - #end if +## create symlinks to input datasets +ln -s '$flow' flow.dat && +#if $oligo.add == "yes": + ln -s '$oligo.oligos' oligo.oligos.dat && +#end if - echo 'trim.flows( - flow=flow.dat, - minflows=$minflows, - maxflows=$maxflows, - #if $maxhomop: - maxhomop=$maxhomop, - #end if - order=$order, - signal=$signal, - noise=$noise, - #if $oligo.add == "yes": - oligos=oligo.oligos.dat, - bdiffs=$oligo.bdiffs, - pdiffs=$oligo.pdiffs, - tdiffs=$oligo.tdiffs, - ldiffs=$oligo.ldiffs, - sdiffs=$oligo.sdiffs, - #end if - fasta=$fasta, - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log - ## prevent these two files from being gathered into collection - && mv flow.trim.flow flow.trim - && mv flow.scrap.flow flow.scrap +echo 'trim.flows( + flow=flow.dat, + minflows=$minflows, + maxflows=$maxflows, + #if $maxhomop: + maxhomop=$maxhomop, + #end if + order=$order, + signal=$signal, + noise=$noise, + #if $oligo.add == "yes": + oligos=oligo.oligos.dat, + bdiffs=$oligo.bdiffs, + pdiffs=$oligo.pdiffs, + tdiffs=$oligo.tdiffs, + ldiffs=$oligo.ldiffs, + sdiffs=$oligo.sdiffs, + #end if + fasta=$fasta, + processors='\${GALAXY_SLOTS:-8}' +)' +| sed 's/ //g' ## mothur trips over whitespace +| mothur +| tee mothur.out.log + +## prevent these two files from being gathered into collection +&& mv flow.trim.flow flow.trim +&& mv flow.scrap.flow flow.scrap ]]></command> <inputs> <param name="flow" type="data" format="mothur.sff.flow" label="flow - flowgram data" help="Use sffinfo to generate flow data from an sff file"/> @@ -119,8 +120,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -130,7 +130,6 @@ .. _trim.flows: https://www.mothur.org/wiki/Trim.flows -]]> - </help> + ]]></help> <expand macro="citations"/> </tool>