Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/consensus.seqs.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 | 5265aa9067e0 |
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<tool id="mothur_consensus_seqs" name="Consensus.seqs" version="1.19.0" force_history_refresh="True"> <description>Find a consensus sequence for each OTU or phylotype</description> <command interpreter="python"> mothur_wrapper.py --cmd='consensus.seqs' --outputdir='$logfile.extra_files_path' --fasta=$fasta #if $name.__str__ != "None" and len($name.__str__) > 0: --name=$name #end if #if $otu.use == 'yes': --list=$otu.list #if $otu.label.__str__ != "None" and len($otu.label.__str__) > 0: --label='$otu.label' #end if --result='^mothur.\S+\.logfile$:'$logfile --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.(((unique|[0-9.]*)\.)?cons\.fasta)$:fasta','^\S+?\.(((unique|[0-9.]*)\.)?cons\.names)$:names','^\S+?\.(((unique|[0-9.]*)\.)?cons\.summary)$:tabular' #else --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.cons\.summary$:'$summary,'^\S+\.cons\.fasta$:'$cons_fasta #end if </command> <inputs> <param name="fasta" type="data" format="fasta" label="fasta - Sequences to Bin" help="Sequences must be the same length"/> <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <conditional name="otu"> <param name="use" type="select" label="Consensus sequence"> <option value="no">Single consensus sequence</option> <option value="yes">Consensus sequence for each OTU in list</option> </param> <when value="no"/> <when value="yes"> <param name="list" type="data" format="list" label="list - OTU List"/> <param name="label" type="select" optional="true" label="label - OTU Labels" multiple="true"> <options from_dataset="list"> <column name="name" index="0"/> <column name="value" index="0"/> </options> </param> </when> </conditional> <!-- --> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> <data format="tabular" name="summary" label="${tool.name} on ${on_string}: cons.summary"> <filter>otu['use'] == 'no'</filter> </data> <data format="fasta" name="cons_fasta" label="${tool.name} on ${on_string}: cons.fasta"> <filter>otu['use'] == 'no'</filter> </data> </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 consensus.seqs_ command can be used in 2 ways: create a consensus sequence from a fastafile, or with a listfile create a consensus sequence for each otu. Sequences must be aligned. .. _consensus.seqs: http://www.mothur.org/wiki/Consensus.seqs </help> </tool>