Mercurial > repos > iuc > mothur_rarefaction_single
diff rarefaction.single.xml @ 0:ee20e83b2a92 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d
| author | iuc |
|---|---|
| date | Fri, 19 May 2017 04:54:15 -0400 |
| parents | |
| children | 871f24df79d8 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/rarefaction.single.xml Fri May 19 04:54:15 2017 -0400 @@ -0,0 +1,106 @@ +<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"/> + </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> + <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> + <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"/> +</tool>