Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/read.otu.xml @ 1:fcc0778f6987
Migrated tool version 1.16.0 from old tool shed archive to new tool shed repository
author | jjohnson |
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date | Tue, 07 Jun 2011 17:35:35 -0400 |
parents | 3202a38e44d9 |
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<tool id="mothur_read_otu" name="Read.otu" version="1.16.0" force_history_refresh="True"> <description>Read OTU list and group to create a shared file</description> <command interpreter="python"> mothur_wrapper.py --cmd='read.otu' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.shared:'$shared --outputdir='$logfile.extra_files_path' #if $show_rabund.value == True: --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.((\S+)\.rabund)$:rabund' #end if --list=$otu --group=$otu_group #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if </command> <inputs> <param name="otu" type="data" format="list" label="list - OTU List"/> <param name="otu_group" type="data" format="groups" label="group - Group file for the OTU List"/> <param name="label" type="select" label="label - OTU Labels" optional="true" multiple="true"> <options from_dataset="otu"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="show_rabund" type="boolean" truevalue="yes" falsevalue="no" checked="true" label="Put Group rabund files in your history"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="shared" name="shared" label="${tool.name} on ${on_string}: shared" /> </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 read.otu_ command is called before most of the OTU based mothur commands. It is included here explicitly to allow the creatation of a shared file from OTU list and group files. .. _read.otu: http://www.mothur.org/wiki/Read.otu </help> </tool>