annotate rarefaction.single.xml @ 6:b5bcc4bf53d1 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"

<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&lt;designation&gt;.*)" 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>