Mercurial > repos > iuc > mothur_chop_seqs
diff chop.seqs.xml @ 4:2029b3939394 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4648c7574a78601e03ae6a318cbcd5b492a8a9f4
| author | iuc |
|---|---|
| date | Wed, 14 Feb 2018 09:16:51 -0500 |
| parents | 35eefac6662c |
| children | 92bebd51ca52 |
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--- a/chop.seqs.xml Fri Sep 08 13:23:28 2017 -0400 +++ b/chop.seqs.xml Wed Feb 14 09:16:51 2018 -0500 @@ -7,47 +7,47 @@ <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 "$group" group.dat && - ln -s "$count" count.dat && +## create symlinks to input datasets +ln -s '$fasta' fasta.dat && +ln -s '$name' name.dat && +ln -s '$group' group.dat && +ln -s '$count' count.dat && - echo 'chop.seqs( - fasta=fasta.dat, - numbases=$numbases, - keep=$keep, - countgaps=$countgaps, - short=$short, - #if $name: - name=name.dat, - #end if - #if $group: - group=group.dat, - #end if - #if $count: - count=count.dat, - #end if - processors='\${GALAXY_SLOTS:-8}' - )' - | sed 's/ //g' ## mothur trips over whitespace - | mothur - | tee mothur.out.log +echo 'chop.seqs( + fasta=fasta.dat, + numbases=$numbases, + keep=$keep, + countgaps=$countgaps, + short=$short, + #if $name: + name=name.dat, + #end if + #if $group: + group=group.dat, + #end if + #if $count: + count=count.dat, + #end if + 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,mothur.align" label="fasta - Sequences to be chopped"/> - <param name="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/> - <param name="keep" type="select" label="keep - Part of the sequence to keep"> + <param argument="fasta" type="data" format="fasta,mothur.align" label="fasta - Sequences to be chopped"/> + <param argument="numbases" type="integer" value="10" label="numbases - Number of bases to keep"/> + <param argument="keep" type="select" label="keep - Part of the sequence to keep"> <option value="front">front</option> <option value="back">back</option> </param> - <param name="countgaps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="countgaps - Count gaps as bases"/> - <param name="short" type="boolean" truevalue="true" falsevalue="false" checked="false" label="short - keep sequences that are too short to chop"/> - <param name="name" type="data" format="mothur.names" optional="true" label="name file"/> - <param name="group" type="data" format="mothur.groups" optional="true" label="group file"/> - <param name="count" type="data" format="mothur.count_table" optional="true" label="count file"/> + <param argument="countgaps" type="boolean" truevalue="true" falsevalue="false" checked="false" label="countgaps - Count gaps as bases"/> + <param argument="short" type="boolean" truevalue="true" falsevalue="false" checked="false" label="short - keep sequences that are too short to chop"/> + <param argument="name" type="data" format="mothur.names" optional="true" label="name file"/> + <param argument="group" type="data" format="mothur.groups" optional="true" label="group file"/> + <param argument="count" type="data" format="mothur.count_table" optional="true" label="count file"/> </inputs> <outputs> <expand macro="logfile-output"/> @@ -61,8 +61,7 @@ <expand macro="logfile-test"/> </test> </tests> - <help> -<![CDATA[ + <help><![CDATA[ @MOTHUR_OVERVIEW@ @@ -73,7 +72,7 @@ .. _chop.seqs: https://www.mothur.org/wiki/Chop.seqs v1.20.0: Updated to 1.33. Added name, group and count options for mothur version 1.31.0 -]]> - </help> + + ]]></help> <expand macro="citations"/> </tool>