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<tool profile="16.07" id="mothur_tree_shared" name="Tree.shared" version="@WRAPPER_VERSION@.0">
    <description>Generate a newick tree for dissimilarity among groups</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <expand macro="version_command"/>
    <command detect_errors="aggressive"><![CDATA[
        echo 'tree.shared(
            #if $input.source == "shared":
                shared=$input.dist,
                #if $input.groups:
                    groups=${ str($input.groups).replace(",","-") },
                #end if
                #if $input.label:
                    label=${ str($input.label).replace(",","-") },
                #end if
                #if $input.subsampling.use == "yes":
                    #if $input.subsampling.subsample:
                        subsample=$input.subsampling.subsample,
                    #else
                        subsample=T,
                    #end if
                    #if $input.subsampling.iters:
                        iters="$input.subsampling.iters,
                    #end if
                #end if
            #elif $input.source == "column":
                column=$input.dist,
                name=$input.name,
            #elif $input.source == "phylip":
                phylip=$input.dist,
                #if $input.name:
                    name=$input.name,
                #end if
            #else
                count=$input.name,
            #end if
            #if $calc:
                calc=${ str($calc).replace(",","-") },
            #end if
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur &&

        ## move output files to correct destination
        prefix='$input.dist' &&
        #if $input.source == 'shared':
            mv \${prefix%.dat}*.tre . &&
        #else
            mv \${prefix%.dat}*.tre '$tre' &&
        #end if
        mv mothur.*.logfile '$logfile'
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="source" type="select" label="Select input format">
                <option value="shared">OTU Shared</option>
                <option value="column">Pairwise Column Distance Matrix</option>
                <option value="phylip">Phylip Distance Matrix</option>
                <option value="count">Count file</option>
            </param>
            <when value="column">
                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
                <param name="name" type="data" format="mothur.names" label="name - Sequences Name reference"/>
            </when>
            <when value="phylip">
                <param name="dist" type="data" format="mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
                <param name="name" type="data" format="mothur.names" optional="true" label="name - Names"/>
            </when>
            <when value="shared">
                <param name="dist" type="data" format="mothur.shared" label="shared - OTU Shared"/>
                <param name="label" type="select" label="label - OTU Labels" multiple="true">
                    <options>
                        <filter type="data_meta" ref="dist" key="labels"/>
                    </options>
                </param>
                <param name="groups" type="select" label="groups - Groups to consider" multiple="true">
                    <options>
                        <filter type="data_meta" ref="dist" key="groups"/>
                    </options>
                </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="" min="1" optional="true" label="iters - Number of iterations to try (default 1000)"/>
                    </when>
                    <when value="no"/>
                </conditional>
            </when>
            <when value="count">
                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
                <param name="name" type="data" format="mothur.count_table" label="count - count_table file"/>
            </when>
        </conditional>
        <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>
    </inputs>
    <outputs>
        <data name="logfile" format="txt" label="${tool.name} on ${on_string}: logfile"/>
        <data name="tre" format="mothur.tre" label="${tool.name} on ${on_string}: tre">
            <filter>input['source'] != 'shared'</filter>
        </data>
        <collection name="trefiles" type="list" label="${tool.name} on ${on_string}: tre">
            <filter>input['source'] == 'shared'</filter>
        	<discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.tre" format="mothur.tre"/>
        </collection>
    </outputs>
    <tests>
        <test><!-- test with phylip and defaults -->
            <param name="source" value="phylip"/>
            <param name="dist" value="env.dist"/>
            <output name="tre" md5="c74a88ed448aad2d07059eda0b4161e9" ftype="mothur.tre"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with shared and subsampling -->
            <param name="source" value="shared"/>
            <param name="dist" value="amazon.an.shared"/>
            <param name="use" value="yes"/>
            <param name="calc" value="jclass"/>
            <output_collection name="trefiles" count="108">
                <element name="jclass.0.32.all" md5="b8adfa6e41397b3815768f987836d102" ftype="mothur.tre"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with shared and label and group select and all calculators -->
            <param name="source" value="shared"/>
            <param name="dist" value="amazon.an.shared"/>
            <param name="label" value="0.05,0.22,0.32"/>
            <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,structchord,structeuclidean,structkulczynski,structpearson,sharednseqs,sharedobserved"/>
            <output_collection name="trefiles" count="117">
                <element name="canberra.0.32" md5="477b061d738d24a7476dd4c90d9666cf" ftype="mothur.tre"/>
            </output_collection>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with column and name file -->
            <param name="source" value="column"/>
            <param name="dist" value="amazon.pair.dist"/>
            <param name="name" value="amazon1.names"/>
            <output name="tre" md5="33cc8cb433f123e49b33b998186b74ed" ftype="mothur.tre"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documenation**

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

.. _tree.shared: http://www.mothur.org/wiki/Tree.shared

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