<tool profile="16.07" id="mothur_dist_shared" name="Dist.shared" version="@WRAPPER_VERSION@.0">
    <description>Generate a phylip-formatted dissimilarity distance matrix among multiple groups</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        ## create symlinks to input datasets
        ln -s "$otu" otu.dat &&

        echo 'dist.shared(
            shared=otu.dat,
            #if $label:
                label=${ str($label).replace(",","-") },
            #end if
            #if $groups:
                groups=${ str($groups).replace(",","-") },
            #end if
            #if $calc:
                calc=${ str($calc).replace(",","-") },
            #end if
            #if $subsampling.use == "yes":
                #if $subsampling.subsample:
                    subsample=$subsampling.subsample,
                #end if
                iters=$subsampling.iters,
            #end if
            output=$output,
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
        <param name="label" type="select" label="label - OTU Labels to calculate" multiple="true">
            <expand macro="labeloptions"/>
        </param>
        <param name="groups" type="select" label="groups - Groups to analyze" multiple="true">
            <options>
                <filter type="data_meta" ref="otu" key="groups"/>
            </options>
        </param>
        <param name="calc" type="select" label="calc - Calculators (Uses defaults if none selected)" multiple="true">
            <option value="sharedsobs">sharedsobs - Shared community richness the observed richness shared between two or more samples</option>
            <option value="sharedchao">sharedchao - Shared community richness the two or more sample shared Chao1 richness estimator</option>
            <option value="sharedace">sharedace - Shared community richness the two sample shared ACE richness estimator</option>
            <option value="anderberg">anderberg - Community Membership Similarity the Anderberg similarity coefficient</option>
            <option value="jclass" selected="true">jclass - Community Membership Similarity the traditional Jaccard similarity coefficient based on the observed richness</option>
            <option value="jest">jest - Community Membership Similarity the Jaccard similarity coefficient based on the Chao1 estimated richnesses</option>
            <option value="kulczynski">kulczynski - Community Membership Similarity the Kulczynski similarity coefficient</option>
            <option value="kulczynskicody">kulczynskicody - Community Membership Similarity the Kulczynski-Cody similarity coefficient</option>
            <option value="kstest">kstest - Community Membership Similarity Kolmogorov-Smirnov test</option>
            <option value="lennon">lennon - Community Membership Similarity the Lennon similarity coefficient</option>
            <option value="ochiai">ochiai - Community Membership Similarity the Ochiai similarity coefficient</option>
            <option value="sorclass">sorclass - Community Membership Similarity the Sorenson similarity coefficient based on the observed richness</option>
            <option value="sorest">sorest - Community Membership Similarity the Sorenson similarity coefficient based on the Chao1 estimated richnesses</option>
            <option value="whittaker">whittaker - Community Membership Similarity the Whittaker similarity coefficient</option>
            <option value="hamming">hamming - Community Membership Similarity -</option>
            <option value="memchi2">memchi2 - Community Membership Similarity -</option>
            <option value="memchord">memchord - Community Membership Similarity -</option>
            <option value="memeuclidean">memeuclidean - Community Membership Similarity -</option>
            <option value="mempearson">mempearson - Community Membership Similarity -</option>
            <option value="braycurtis">braycurtis - Community Structure Similarity the Bray-Curtis similarity coefficient</option>
            <option value="jabund">jabund - Community Structure Similarity the abundance-based Jaccard similarity coefficient</option>
            <option value="morisitahorn">morisitahorn - Community Structure Similarity the Morisita-Horn similarity coefficient</option>
            <option value="sorabund">sorabund - Community Structure Similarity the abundance-based Sorenson similarity coefficient</option>
            <option value="thetan">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>
            <option value="canberra">canberra - Community Structure Similarity -</option>
            <option value="gower">gower - Community Structure Similarity -</option>
            <option value="hellinger">hellinger - Community Structure Similarity -</option>
            <option value="manhattan">manhattan - Community Structure Similarity -</option>
            <option value="odum">odum - Community Structure Similarity -</option>
            <option value="soergel">soergel - Community Structure Similarity -</option>
            <option value="spearman">spearman - Community Structure Similarity -</option>
            <option value="speciesprofile">speciesprofile - Community Structure Similarity -</option>
            <option value="structchi2">structchi2 - Community Structure Similarity -</option>
            <option value="structchord">structchord - Community Structure Similarity -</option>
            <option value="structeuclidean">structeuclidean - Community Structure Similarity -</option>
            <option value="structkulczynski">structkulczynski - Community Structure Similarity -</option>
            <option value="structpearson">structpearson - Community Structure Similarity -</option>
            <option value="sharednseqs">sharednseqs - Utility the number of sequences in two samples</option>
            <option value="sharedobserved">sharedobserved - Utility the number of sequences in two samples</option>
        </param>
        <conditional name="subsampling">
            <param name="use" type="select" label="subsample">
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="yes">
                <param name="subsample" type="integer" value="" min="0" optional="true" label="subsample (defaults to the size of the smallest group)" help="Should not exceed the number of sequences in any group"/>
                <param name="iters" type="integer" value="1000" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
            </when>
            <when value="no"/>
        </conditional>
        <param name="output" type="select" label="output - Distance Matrix Output Format" help="A Distance Matrix will be generated for each calculator label pair">
            <option value="lt" selected="true">Phylip formatted Lower Triangle Matrix</option>
            <option value="square">Phylip formatted Square Matrix</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="distfiles" type="list" label="${tool.name} on ${on_string}: dist files">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.dist" format="mothur.dist"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with defaults -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output_collection name="distfiles" count="72">
                <element name="thetayc.0.33.lt" md5="c707e43f14c2022f4027e6a2495cbae8" ftype="mothur.dist"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with label,group select and all calculators -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="label" value="0.05,0.22"/>
            <param name="groups" value="forest,pasture"/>
            <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,structeuclidean,structpearson,sharednseqs,sharedobserved"/>
            <output_collection name="distfiles" count="74">
                <element name="gower.0.22.lt" md5="209dbf7e9f1e13753524905f64c8e3b7" ftype="mothur.dist"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with subsampling -->
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="use" value="yes"/>
            <param name="subsample" value="10"/>
            <param name="iters" value="42"/>
            <param name="label" value="0.03,0.33"/>
            <param name="calc" value="canberra"/>
            <param name="output" value="square"/>
            <output_collection name="distfiles" count="6">
                <element name="canberra.0.33.square.std" ftype="mothur.dist">
                    <assert_contents>
                        <has_text text="forest"/>
                        <has_text text="pasture"/>
                    </assert_contents>
                </element>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documenation**

The dist.shared_ command will generate a phylip-formatted_distance_matrix_ that describes the dissimilarity (1-similarity) among multiple groups from a shared_ file. For calc parameter choices see: http://www.mothur.org/wiki/Calculators

.. _phylip-formatted_distance_matrix: http://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _shared: http://www.mothur.org/wiki/Shared_file
.. _dist.shared: http://www.mothur.org/wiki/Dist.shared

v1.26.0: Updated to Mothur 1.33. Omitted calculators since they do not appear to be available.

]]>
    </help>
    <expand macro="citations"/>
</tool>