Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/cluster.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_cluster" name="Cluster" version="1.16.0"> <description>Assign sequences to OTUs (Operational Taxonomic Unit)</description> <command interpreter="python"> mothur_wrapper.py --cmd='cluster' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist --outputdir='$logfile.extra_files_path' --READ_cmd='read.dist' #if $matrix.format == "column": --READ_column=$matrix.dist --READ_name=$matrix.name #elif $matrix.format == "phylip": --READ_phylip=$matrix.dist #if $matrix.name.__str__ != "None" and len($matrix.name.__str__) > 0: --READ_name=$matrix.name #end if #end if $sim #if float($cutoff.__str__) > 0.0: --READ_cutoff=$cutoff #end if $hard #if len($precision.__str__) > 0: --READ_precision=$precision #end if #if len($method.__str__) > 0: --method=$method #end if </command> <inputs> <conditional name="matrix"> <param name="format" type="select" label="Select a Distance Matrix Format" help=""> <option value="column">Pairwise Column Matrix</option> <option value="phylip">Phylip Distance Matrix</option> </param> <when value="column"> <param name="dist" type="data" format="pair.dist" label="read.dist(column=) - Distance Matrix"/> <param name="name" type="data" format="names" label="read.dist(name=) - Sequences Name reference"/> </when> <when value="phylip"> <param name="dist" type="data" format="lower.dist,square.dist" label="read.dist(phylip=) - Distance Matrix"/> <param name="name" type="data" format="names" optional="true" label="read.dist(name=) - Sequences Name reference"/> </when> </conditional> <!-- ? conditional - to hide complexity --> <param name="method" type="select" label="method - Select a Clustering Method" help=""> <option value="furthest" selected="true">Furthest neighbor</option> <option value="nearest">Nearest neighbor</option> <option value="average">Average neighbor</option> <option value="weighted">Weighted</option> </param> <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/> <param name="hard" type="boolean" checked="false" truevalue="--hard=true" falsevalue="" label="hard - Use hard cutoff instead of rounding" help=""/> <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths"> <option value="10">.1</option> <option value="100" selected="true">.01</option> <option value="1000">.001</option> <option value="10000">.0001</option> <option value="100000">.00001</option> <option value="1000000">.000001</option> </param> <param name="sim" type="boolean" checked="false" truevalue="--READ_sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" help=""/> </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 cluster_ command assign sequences to OTUs (Operational Taxonomy Unit). .. _cluster: http://www.mothur.org/wiki/Cluster </help> </tool>