Mercurial > repos > iuc > mothur_rarefaction_single
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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit ff56a4c9218ddea84ff5cd72fd98c62db212465d"
author | iuc |
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date | Thu, 05 Nov 2020 22:44:30 +0000 |
parents | 8091da04fbac |
children | 47264675a4ea |
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<tool profile="16.07" id="mothur_rarefaction_single" name="Rarefaction.single" version="@WRAPPER_VERSION@.0"> <description>Generate intra-sample rarefaction curves for OTUs</description> <macros> <import>macros.xml</import> </macros> <expand macro="requirements"/> <expand macro="stdio"/> <expand macro="version_command"/> <command><![CDATA[ @SHELL_OPTIONS@ ## create symlinks to input datasets ln -s '$otu' otu.dat && echo 'rarefaction.single( #if $otu.is_of_type("mothur.rabund"): rabund=otu.dat, #elif $otu.is_of_type("mothur.sabund"): sabund=otu.dat, #elif $otu.is_of_type("mothur.shared"): shared=otu.dat, #elif $otu.is_of_type("mothur.list"): list=otu.dat, #end if #if $label: label=${ str($label).replace(",","-") }, #end if calc=${ str($calc).replace(",","-") }, abund=$abund, iters=$iters, freq=$freq, processors='\${GALAXY_SLOTS:-8}' )' | sed 's/ //g' ## mothur trips over whitespace | mothur | tee mothur.out.log ## rename output from sobs calculator to be consistent with others #if 'sobs' in str($calc).split(','): && mv otu\.*rarefaction otu.r_sobs #end if ]]></command> <inputs> <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund,mothur.shared" label="list,rabund,sabund,shared - OTU List"/> <param name="label" type="select" label="label - OTU Labels" multiple="true"> <expand macro="labeloptions"/> </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" min="0" label="abund - ACE Estimator threshold for abundant versus rare OTUs"/> <param name="iters" type="integer" value="1000" min="0" label="iters - Number of randomizations"/> <param name="freq" type="float" value="100" min="0" max="100" label="freq - Reporting frequency" help="if between 0 and 1 the fraction of sequences to sample, if greater than one - report every n iterations"/> <expand macro="param-savelog"/> </inputs> <outputs> <expand macro="logfile-output"/> <collection name="rarefactioncurves" type="list" label="${tool.name} on ${on_string}: rarefaction curves"> <discover_datasets pattern=".*?(\.groups)?\.r_(?P<designation>.*)" format="tabular"/> </collection> </outputs> <tests> <test><!-- test with default values --> <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> <output_collection name="rarefactioncurves" count="1"> <element name="sobs" md5="c4c1f1970edf87ea5103e0704130f079" ftype="tabular"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> <test><!-- test with all calculators and subset of labels --> <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/> <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,coverage,simpson,invsimpson,shannon,npshannon,nseqs"/> <param name="label" value="0.03,0.05,0.36,0.55"/> <output_collection name="rarefactioncurves" count="15"> <element name="simpson" md5="8d6b7ad9a68c30c882e93b17d343042a" ftype="tabular"/> </output_collection> <param name="savelog" value="true"/> <expand macro="logfile-test"/> </test> </tests> <help><![CDATA[ @MOTHUR_OVERVIEW@ **Command Documentation** 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: https://www.mothur.org/wiki/Calculators .. _rarefaction.single: https://www.mothur.org/wiki/Rarefaction.single ]]></help> <expand macro="citations"> <citation type="bibtex"><![CDATA[ @book{magurran2013measuring, title={Measuring biological diversity}, author={Magurran, Anne E}, year={2013}, publisher={John Wiley \& Sons} } ]]></citation> </expand> </tool>