view collect.single.xml @ 5:7f212a2a4a3b draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7f7605c2c8d8e92f3369dfdc290e5d8d06fa409a

<tool profile="16.07" id="mothur_collect_single" name="Collect.single" version="@WRAPPER_VERSION@.0">
    <description>Generate collector's 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 'collect.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,
    freq=$freq
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
&& rm otu.dat  ## don't want this collected into datacollection
    ]]></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" selected="true">ace - Community richness the ACE estimator</option>
            <option value="bootstrap">bootstrap - Community richness the bootstrap estimator</option>
            <option value="chao" selected="true">chao - Community richness the Chao1 estimator</option>
            <option value="jack" selected="true">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="bergerparker">bergerparker - Community diversity the Berger-Parker index</option>
            <option value="coverage">coverage - Community diversity the sampling coverage </option>
            <option value="goodscoverage">goodscoverage - Community diversity the Good's estimate of sampling coverage </option>
            <option value="simpson" selected="true">simpson - Community diversity the Simpson index</option>
            <option value="invsimpson">invsimpson - Community diversity the Simpson index</option>
            <option value="qstat">qstat - Community diversity the Q statistic</option>
            <option value="shannon" selected="true">shannon - Community diversity the Shannon index</option>
            <option value="npshannon" selected="true">npshannon - Community diversity the non-parametric Shannon index</option>
            <option value="boneh">boneh - Estimator Boneh's estimator</option>
            <option value="efron">efron - Estimator Efron's estimator</option>
            <option value="shen">shen - Estimator Shen's estimator</option>
            <option value="solow">solow - Estimator Solow's estimator</option>
            <option value="logseries">logseries - Statistical distribution tests whether observed data follow the log series distribution</option>
            <option value="geometric">geometric - Statistical distribution tests whether observed data follow the geometric series distribution</option>
            <option value="bstick">bstick - Statistical distribution tests whether observed data follow the broken stick distribution</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 (default 10)"/>
        <param name="freq" type="float" value="100" min="0" label="freq - frequency for output (default is every 100 sequences)"
            help="Use a decimal between 0 and 1 to set the frequency as a percentage of the number of sequences"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="calcfiles" type="list" label="${tool.name} on ${on_string}: calculators">
            <discover_datasets pattern="otu\.(?P&lt;designation&gt;.*)" format="tabular"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test default settings -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <output_collection name="calcfiles" count="7">
                <element name="shannon" md5="0a9c8a52f89898c3b7b7b2dfa24a4521" ftype="tabular"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with label select and all calculators -->
            <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
            <param name="label" value="0.36,0.38,0.41"/>
            <param name="calc" value="ace,bootstrap,chao,jack,sobs,simpsoneven,shannoneven,heip,smithwilson,bergerparker,coverage,goodscoverage,simpson,invsimpson,qstat,shannon,npshannon,boneh,efron,shen,solow,logseries,geometric,bstick,nseqs"/>
            <output_collection name="calcfiles" count="25">
                <element name="bstick" md5="a38d430c52768efca597e5b41fc1d84b" ftype="tabular"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@


**Command Documentation**

The collect.single_ command generates collector's curves using calculators_, that describe the richness, diversity, and other features of individual samples. Collector's curves describe how richness or diversity change as you sample additional individuals. If a collector's curve becomes parallel to the x-axis, you can be reasonably confident that you have done a good job of sampling and can trust the last value in the curve. Otherwise, you need to keep sampling.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators

.. _calculators: https://www.mothur.org/wiki/Calculators
.. _collect.single: https://www.mothur.org/wiki/Collect.single

    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1128/AEM.00474-06</citation>
    </expand>
</tool>