Mercurial > repos > jjohnson > mothur_toolsuite
view mothur/tools/mothur/rarefaction.single.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 | bfbaf823be4c |
children | 95d75b35e4d2 |
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<tool id="mothur_rarefaction_single" name="Rarefaction.single" version="1.20.0" force_history_refresh="True"> <description>Generate intra-sample rarefaction curves for OTUs</description> <command interpreter="python"> mothur_wrapper.py --cmd='rarefaction.single' --result='^mothur.\S+\.logfile$:'$logfile --outputdir='$logfile.extra_files_path' #if $as_datasets.__str__ == 'yes': --datasetid='$logfile.id' --new_file_path='$__new_file_path__' --new_datasets='^\S+?\.(((\S+)\.)?(rarefaction|r_\w*))$:tabular' #end if #if isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('shared').__class__): --shared=$otu #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('rabund').__class__): --rabund=$otu #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('sabund').__class__): --sabund=$otu #elif isinstance($otu.datatype, $__app__.datatypes_registry.get_datatype_by_extension('list').__class__): --list=$otu #end if #if $label.__str__ != "None" and len($label.__str__) > 0: --label='$label' #end if #if $calc.__str__ != "None" and len($calc.__str__) > 0: --calc='$calc' #end if #if int($abund.__str__) > 0: --abund=$abund #end if #if int($iters.__str__) > 0: --iters=$iters #end if #if float($freq.__str__) > 0: --freq=$freq #end if --processors=8 </command> <inputs> <param name="otu" type="data" format="list,rabund,sabund,shared" label="list,rabund,sabund,shared - OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <options> <filter type="data_meta" ref="otu" key="labels" /> </options> </param> <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true"> <option value="ace">ace - Community richness the ACE estimator</option> <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option> <option value="chao">chao - Community richness the Chao1 estimator</option> <option value="jack">jack - Community richness the jackknife estimator</option> <option value="sobs" selected="true">sobs - Community richness the observed richness</option> <option value="simpsoneven">simpsoneven - Community evenness a Simpson index-based measure of evenness</option> <option value="shannoneven">shannoneven - Community evenness a Shannon index-based measure of evenness</option> <option value="heip">heip - Community evenness Heip's metric of community evenness</option> <option value="smithwilson">smithwilson - Community evenness Smith and Wilson's metric of community evenness</option> <option value="coverage">coverage - Community diversity the sampling coverage </option> <option value="simpson">simpson - Community diversity the Simpson index</option> <option value="invsimpson">invsimpson - Community diversity the Simpson index</option> <option value="shannon">shannon - Community diversity the Shannon index</option> <option value="npshannon">npshannon - Community diversity the non-parametric Shannon index</option> <option value="nseqs">nseqs - Utility the number of sequences in a sample</option> </param> <param name="abund" type="integer" value="10" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/> <param name="iters" type="integer" value="0" label="iters - Number of randomizations"/> <param name="freq" type="float" value="0.0" label="freq - Reporting frequency" help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/> <param name="as_datasets" type="boolean" truevalue="yes" falsevalue="no" checked="True" label="Create a new history dataset for each label and calculator"/> </inputs> <outputs> <data format="html" name="logfile" label="${tool.name} on ${on_string}: logfile" /> </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 rarefaction.single_ command generates intra-sample rarefaction curves using a re-sampling without replacement approach. Rarefaction curves provide a way of comparing the richness observed in different samples. For calc parameter choices see: http://www.mothur.org/wiki/Calculators .. _rarefaction.single: http://www.mothur.org/wiki/Rarefaction.single </help> </tool>