Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/cluster.split.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 | 4f797d3eee3a |
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<tool id="mothur_cluster_split" name="Cluster.split" version="1.19.0"> <description>Assign sequences to OTUs (Operational Taxonomic Unit) splits large matrices</description> <command interpreter="python"> mothur_wrapper.py --cmd='cluster.split' --result='^mothur.\S+\.logfile$:'$logfile,'^\S+\.sabund$:'$sabund,'^\S+\.rabund$:'$rabund,'^\S+\.list$:'$otulist,'^\S+\.dist$:'$dist_out --outputdir='$logfile.extra_files_path' #if $splitby.splitmethod == "distance": #if $splitby.matrix.format == "column": --column=$splitby.matrix.dist --name=$splitby.matrix.name #elif $splitby.matrix.format == "phylip": --phylip=$splitby.matrix.dist #if $splitby.matrix.name.__str__ != "None" and len($splitby.matrix.name.__str__) > 0: --name=$splitby.matrix.name #end if #end if --splitmethod=$splitby.splitmethod #elif $splitby.splitmethod == "classify": --column=$splitby.dist --name=$splitby.name --taxonomy=$splitby.taxonomy #if $splitby.taxlevel > 1: --taxlevel=$splitby.taxlevel #end if --splitmethod=$splitby.splitmethod #elif $splitby.splitmethod == "fasta": --fasta=$splitby.fasta --name=$splitby.name --taxonomy=$splitby.taxonomy #if $splitby.taxlevel > 1: --taxlevel=$splitby.taxlevel #end if --splitmethod=$splitby.splitmethod #end if #if len($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 $large --processors=1 </command> <inputs> <conditional name="splitby"> <param name="splitmethod" type="select" label="Split by" help=""> <option value="distance">Distance</option> <option value="classify">Classification</option> <option value="fasta">Classification using fasta</option> </param> <when value="distance"> <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="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 - Sequences Name reference"/> </when> </conditional> </when> <when value="classify"> <param name="dist" type="data" format="pair.dist" label="column - Distance Matrix"/> <param name="name" type="data" format="names" label="name - Sequences Name reference"/> <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/> <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/> </when> <when value="fasta"> <param name="fasta" type="data" format="fasta" label="fasta - Sequences"/> <param name="name" type="data" format="names" label="name - Sequences Name reference"/> <param name="taxonomy" type="data" format="seq.taxonomy" label="taxonomy - Taxonomy (from Classify.seqs)"/> <param name="taxlevel" type="integer" value="1" label="taxlevel - taxonomy level for split (default=1)" help="taxonomy level you want to use to split the distance file, default=1, meaning use the first taxon in each list"/> </when> </conditional> <!-- splitby --> <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> </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=true" 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="large" type="boolean" checked="false" truevalue="--large=true" falsevalue="" label="large - distance matrix is too large to fit in RAM" help="If your job fails due to not enough memory error, set this to true to rerun"/> </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 ${on_string}: list (OTU List)"/> <data format="pair.dist" name="dist_out" label="${tool.name} on ${on_string}: Column dist"> <filter>splitby.splitmethod == 'fasta' </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 cluster.split_ command assign sequences to OTUs (Operational Taxonomy Unit). .. _cluster.split: http://www.mothur.org/wiki/Cluster.split </help> </tool>