Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/get.oturep.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 |
children | e990ac8a0f58 |
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<tool id="mothur_get_oturep" name="Get.oturep" version="1.16.0" force_history_refresh="True"> <description>Generate a fasta with a representative sequence for each OTU</description> <command interpreter="python"> mothur_wrapper.py --cmd='get.oturep' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.fasta)$:fasta','^\S+?\.((unique|[0-9.]*)(\S+)\.rep\.names)$:names' --fasta=$fasta --list=$otu_list #if $input.source == 'column': --column=$input.dist --name=$input.name #elif $input.source == 'phylip': --phylip=$input.dist #if $input.name.__str__ != "None" and len($input.name.__str__) > 0: --name=$input.name #end if #end if #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if #if $groups.__str__ != "None" and len($groups.__str__) > 0: --groups=$groups #end if #if $sorted.__str__ != "None" and len($sorted.__str__) > 0: --sorted=$sorted #end if $large </command> <inputs> <!-- get.relabund relabund type should also work --> <param name="fasta" type="data" format="fasta" label="fasta - Fasta"/> <param name="otu_list" type="data" format="list" label="list - OTU List"/> <conditional name="input"> <param name="source" type="select" label="Distance Matrix"> <option value="column">Pairwise Column Distance Matrix</option> <option value="phylip">Phylip Distance Matrix</option> </param> <when value="column"> <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> <param name="name" type="data" format="names" label="name - Sequences Name reference"/> </when> <when value="phylip"> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="name" type="data" format="names" optional="true" label="name - Names"/> </when> </conditional> <param name="group" type="data" format="groups" optional="true" label="group - Group file for the OTU List"/> <param name="groups" type="select" label="groups - Groups to consider" multiple="true"> <options from_dataset="group"> <column name="name" index="1"/> <column name="value" index="1"/> </options> </param> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options from_dataset="otu_list"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> <param name="sorted" type="select" label="sorted - Sort Sequences by"> <option value="">Don't sort</option> <option value="name">Sequence Name</option> <option value="number">Bin Number</option> <option value="size">Bin Size</option> <option value="group">Group</option> </param> <param name="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - Distance Matrix is very Large"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </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 get.oturep_ command generates a fasta-formatted sequence file containing only a representative sequence for each OTU. The opposite of the bin.seqs command. .. _get.oturep: http://www.mothur.org/wiki/Get.oturep </help> </tool>