<tool profile="16.07" id="mothur_phylo_diversity" name="Phylo.diversity" version="@WRAPPER_VERSION@.0">
    <description>Alpha Diversity calculates unique branch length</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 "$tree" tree.dat &&
        ln -s "$name" name.dat &&
        ln -s "$count" count.dat &&
        #if $grouping.use == "yes":
            ln -s "$grouping.group" grouping.group.dat &&
        #end if

        echo 'phylo.diversity(
            tree=tree.dat,
            #if $grouping.use == "yes":
                group=grouping.group.dat,
                #if $grouping.groups:
                    groups=${ str($grouping.groups).replace(",","-") },
                #end if
            #end if
            #if $name:
                name=name.dat,
            #end if
            iters=$iters,
            freq=$freq,
            scale=$scale,
            collect=$collect,
            rarefy=$rarefy,
            summary=$summary,
            #if $count:
                count=count.dat,
            #end if
            processors='\${GALAXY_SLOTS:-8}'
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="tree" type="data" format="mothur.tre" label="tree - Phylogenetic Tree"/>
        <conditional name="grouping">
            <param name="use" type="select" label="Analyze by group using a Group file">
                <option value="no" selected="true">no</option>
                <option value="yes">yes</option>
            </param>
            <when value="yes">
                <param name="group" type="data" format="mothur.groups" label="group - Group file for the tree"/>
                <param name="groups" type="select" multiple="true" label="groups - Groups to display">
                    <help>All groups displayed if none are selected.</help>
                    <options>
                        <filter type="data_meta" ref="group" key="groups"/>
                    </options>
                </param>
            </when>
            <when value="no"/>
        </conditional>
        <param name="name" type="data" format="mothur.names" optional="true" label="name - Sequences Name reference file for the tree"/>
        <param name="iters" type="integer" value="1000" min="0" label="iters - Number of iterations to try (default 1000)"/>
        <param name="freq" type="float" value="100" min="0.0" label="freq - Reporting frequency" help="if between 0 and 100, the percentage of sequences to sample, if greater than one - report every n iterations"/>
        <param name="scale" type="boolean" truevalue="true" falsevalue="false" checked="false" label="scale - Scale output to the number of sequences sampled"/>
        <param name="rarefy" type="boolean" truevalue="true" falsevalue="false" checked="false" label="rarefy - Calculate the rarefaction data"/>
        <param name="summary" type="boolean" truevalue="true" falsevalue="false" checked="true" label="summary - Generate a summary file"/>
        <param name="collect" type="boolean" truevalue="true" falsevalue="false" checked="false" label="collect - Create a collectors curve"/>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="summary_out" format="tabular" from_work_dir="tree*.phylodiv.summary" label="${tool.name} on ${on_string}: summary">
            <filter>summary</filter>
        </data>
        <data name="rarefaction_out" format="tabular" from_work_dir="tree*.phylodiv.rarefaction" label="${tool.name} on ${on_string}: rarefaction">
            <filter>rarefy</filter>
        </data>
        <data name="collectors_out" format="tabular" from_work_dir="tree*.phylodiv" label="${tool.name} on ${on_string}: collectors">
            <filter>collect</filter>
        </data>
    </outputs>
    <tests>
        <test><!-- test with tree file only -->
            <param name="tree" value="treetest.tre" ftype="mothur.tre"/>
            <param name="use" value="no"/>
            <output name="summary_out" md5="a9feb4031094b555baf62e0165dd3637" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with tree file and group file and all outputs -->
            <param name="tree" value="treetest.tre" ftype="mothur.tre"/>
            <param name="use" value="yes"/>
            <param name="group" value="treetest.groups"/>
            <param name="groups" value="orange,green"/>
            <param name="rarefy" value="true"/>
            <param name="collect" value="true"/>
            <output name="summary_out" md5="27375ea164ad39fb56b9606023cae504" ftype="tabular"/>
            <output name="rarefaction_out" ftype="tabular">
                <assert_contents>
                    <has_text text="numSampled"/>
                    <has_text text="orange"/>
                    <has_text text="green"/>
                </assert_contents>
            </output>
            <output name="collectors_out" ftype="tabular">
                <assert_contents>
                    <has_text text="numSampled"/>
                    <has_text text="orange"/>
                    <has_text text="green"/>
                </assert_contents>
            </output>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@


**Command Documentation**

The phylo.diversity_ command calculates alpha diversity as the total of the unique branch length.

.. _phylo.diversity: https://www.mothur.org/wiki/Phylo.diversity

v.1.21.0: Updated to Mothur 1.33, added count parameter

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