Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/cluster.classic.xml @ 27:49058b1f8d3f
Update to mothur version 1.27 and add tool_dependencies.xml to automatically install mothur
author | Jim Johnson <jj@umn.edu> |
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date | Tue, 04 Dec 2012 11:05:19 -0600 |
parents | e990ac8a0f58 |
children | 95d75b35e4d2 |
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<tool id="mothur_cluster_classic" name="Cluster.classic" version="1.27.0"> <description>Assign sequences to OTUs (Dotur implementation)</description> <command interpreter="python"> mothur_wrapper.py --cmd='cluster.classic' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.[fna]n\.sabund$:'$sabund,'^\S+\.[fna]n\.rabund$:'$rabund,'^\S+\.[fna]n\.list$:'$otulist --outputdir='$logfile.extra_files_path' --phylip=$dist #if $name.__str__ != "None" and len($name.__str__) > 0: --name=$name #end if #if $count.__str__ != "None" and len($count.__str__) > 0: --count=$count #end if #if len($method.__str__) > 0: --method=$method #end if #if float($cutoff.__str__) > 0.0: --cutoff=$cutoff #end if $hard #if len($precision.__str__) > 0: --precision=$precision #end if $sim </command> <inputs> <param name="dist" type="data" format="lower.dist,square.dist" label="phylip - Distance Matrix"/> <param name="name" type="data" format="names" optional="true" label="name - Sequences Name reference"/> <param name="count" type="data" format="count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/> <!-- ? conditional - to hide complexity --> <param name="method" type="select" label="method - Select a Clustering Method" help=""> <option value="furthest">Furthest neighbor</option> <option value="nearest">Nearest neighbor</option> <option value="average" selected="true">Average neighbor</option> <option value="weighted">Weighted</option> </param> <param name="cutoff" type="float" value="0.0" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/> <param name="hard" type="boolean" checked="true" truevalue="--hard=true" falsevalue="--hard=false" label="hard - Use hard cutoff instead of rounding" help=""/> <param name="precision" type="select" optional="true" label="precision - Precision for rounding distance values" help="Set higher precision for longer genome scale sequence lengths"> <option value="10">.1</option> <option value="100" selected="true">.01</option> <option value="1000">.001</option> <option value="10000">.0001</option> <option value="100000">.00001</option> <option value="1000000">.000001</option> </param> <param name="sim" type="boolean" checked="false" truevalue="--sim=true" falsevalue="" label="sim - Matrix values are Similary instead of Distance" help=""/> </inputs> <outputs> <data format="html" name="logfile" label="${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="package" version="1.27">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.classic_ command assign sequences to OTUs (Operational Taxonomy Unit). .. _cluster.classic: http://www.mothur.org/wiki/Cluster.classic </help> </tool>