Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/phylotype.xml @ 2:e990ac8a0f58
Migrated tool version 1.19.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:39:06 -0400 |
parents | fcc0778f6987 |
children | 49058b1f8d3f |
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<tool id="mothur_phylotype" name="Phylotype" version="1.19.0"> <description>Assign sequences to OTUs based on taxonomy</description> <command interpreter="python"> mothur_wrapper.py --cmd='phylotype' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist --outputdir='$logfile.extra_files_path' --taxonomy=$taxonomy #if 50 >= int($cutoff.__str__) > 0: --cutoff=$cutoff #end if #if $name.__str__ != "None" and len($name.__str__) > 0: --name='$name' #end if #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if </command> <inputs> <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy"/> <param name="name" type="data" format="names" optional="true" label="name - Names reference file for the taxonomy"/> <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true"> <option value="0">0</option> <option value="1">1</option> <option value="2">2</option> <option value="3">3</option> <option value="4">4</option> <option value="5">5</option> <option value="6">6</option> <option value="7">7</option> <option value="8">8</option> <option value="9">9</option> <option value="10">10</option> </param> <param name="cutoff" type="integer" value="-1" label="cutoff - Truncate the taxonomy at depth (Ignored if < 0)"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="rabund" name="rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/> <data format="sabund" name="sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/> <data format="list" name="otulist" label="${tool.name} on ${on_string}: list (OTU List)"/> </outputs> <requirements> <requirement type="binary">mothur</requirement> </requirements> <tests> </tests> <help> **Mothur Overview** Mothur_, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology and Immunology at The University of Michigan, provides bioinformatics for the microbial ecology community. .. _Mothur: http://www.mothur.org/wiki/Main_Page **Command Documenation** 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: http://www.mothur.org/wiki/List_file .. _rabund: http://www.mothur.org/wiki/Rabund_file .. _sabund: http://www.mothur.org/wiki/Sabund_file .. _phylotype: http://www.mothur.org/wiki/Phylotype </help> </tool>