Mercurial > repos > iuc > mothur_phylotype
view phylotype.xml @ 7:e301ed7e04d8 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"
author | iuc |
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date | Thu, 05 Nov 2020 22:27:25 +0000 |
parents | f750e0c2c7f9 |
children | e6ecdb693d0c |
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<tool profile="16.07" id="mothur_phylotype" name="Phylotype" version="@WRAPPER_VERSION@.0"> <description>Assign sequences to OTUs based on taxonomy</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @SHELL_OPTIONS@ ## create symlinks to input datasets ln -s '$taxonomy' taxonomy.dat && ln -s '$name' name.dat && echo 'phylotype( taxonomy=taxonomy.dat #if $cutoff: ,cutoff=$cutoff #end if #if $name: ,name=name.dat #end if #if $label: ,label=${ str($label).replace(",","-") } #end if )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ]]></command> <inputs> <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/> <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/> <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true"> <option value="0">0</option> <option value="1">1</option> <option value="2">2</option> <option value="3">3</option> <option value="4">4</option> <option value="5">5</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> <option value="9">9</option> <option value="10">10</option> </param> <param name="cutoff" type="integer" value="" min="0" max="50" optional="true" label="cutoff - Truncate the taxonomy at depth (Ignored if < 0)"/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <data name="rabund" format="mothur.rabund" from_work_dir="taxonomy*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> <data name="sabund" format="mothur.sabund" from_work_dir="taxonomy*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> <data name="otulist" format="mothur.list" from_work_dir="taxonomy*.list" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <tests> <test> <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> <output name="rabund" md5="689fb6fd2fb4cd0740fc8b62d7e05556" ftype="mothur.rabund"/> <output name="sabund" md5="62547e84f1d051a16937715433f3d78a" ftype="mothur.sabund"/> <output name="otulist" md5="c808112d524863bbc973dd721ba18a06" ftype="mothur.list"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test> <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/> <param name="label" value="1,4,5"/> <param name="cutoff" value="5"/> <output name="rabund" md5="3d2e3821bef6ecd7eaf0ea62e8692154" ftype="mothur.rabund"/> <output name="sabund" md5="582825c475bffbf7e450156ff26c844a" ftype="mothur.sabund"/> <output name="otulist" md5="424a2c62df2e37b32542731b9631f8ed" ftype="mothur.list"/> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file. .. _list: https://www.mothur.org/wiki/List_file .. _rabund: https://www.mothur.org/wiki/Rabund_file .. _sabund: https://www.mothur.org/wiki/Sabund_file .. _phylotype: https://www.mothur.org/wiki/Phylotype ]]></help> <expand macro="citations"/> </tool>