<tool profile="16.07" id="mothur_collect_shared" name="Collect.shared" version="@WRAPPER_VERSION@.0">
    <description>Generate collector's curves for calculators on 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.shared(
    shared=otu.dat,
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $calc:
        calc=${ str($calc).replace(",","-") },
    #end if
    #if $groups:
        groups=${ str($groups).replace(",","-") },
    #end if
    freq=$freq,
    all=true
)'
| 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.shared" label="shared - OTU Shared"/>
        <param name="label" type="select" multiple="true" label="label - OTU Label filter">
            <expand macro="labeloptions"/>
        </param>
        <param name="groups" type="select" multiple="true" label="groups - Groups filter (uses all groups if none are selected)" help="To filter: select select at least 2 groups">
            <options>
                <filter type="data_meta" ref="otu" key="groups"/>
            </options>
        </param>
        <param name="calc" type="select" multiple="true" label="calc - Calculators (Uses defaults if none are selected)">
            <expand macro="calc-common"/>
            <!-- set default option(s) -->
            <option value="sharedsobs" selected="true">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
            <option value="sharedchao" selected="true">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
            <option value="sharedace" selected="true">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
            <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
            <option value="jest" selected="true">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
            <option value="sorclass" selected="true">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
            <option value="sorest" selected="true">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
            <option value="jabund" selected="true">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
            <option value="sorabund" selected="true">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
            <option value="thetan" selected="true">thetan - Community Structure Similarity the Smith theta similarity coefficient</option>
            <option value="thetayc" selected="true">thetayc - Community Structure Similarity the Yue &amp; Clayton theta similarity coefficient</option>
        </param>
        <param name="freq" type="float" value="100" label="freq - indicates when to output your data"
            help="by default it is set to 100. But you can set it to a percentage of the number of sequence. For example freq=0.10, means 10%" min="0.0" max="100.0"/>
        <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.shared" ftype="mothur.shared"/>
            <output_collection name="calcfiles" count="11">
                <element name="jest" md5="22e97fbdbdadf3c4748d0f7c4d526855" ftype="tabular"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with group and label select and all calculators -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="groups" value="forest,pasture"/>
            <param name="label" value="0.03,0.05,0.22"/>
            <param name="calc" value="sharedsobs,sharedchao,sharedace,anderberg,jclass,jest,kulczynski,kulczynskicody,kstest,lennon,ochiai,sorclass,sorest,whittaker,hamming,memchi2,memchord,memeuclidean,mempearson,braycurtis,jabund,morisitahorn,sorabund,thetan,thetayc,canberra,gower,hellinger,manhattan,odum,soergel,spearman,speciesprofile,structchi2,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs"/>
            <output_collection name="calcfiles" count="39">
                <element name="jest" md5="1289eac7fdcfb42eaf4ee35deb6fb0a4" ftype="tabular"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The collect.shared_ command generates collector's curves for calculators_, which describe the similarity between communities or their shared richness. 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.  For calc parameter choices see: https://www.mothur.org/wiki/Calculators

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

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