<tool profile="16.07" id="mothur_homova" name="Homova" version="@WRAPPER_VERSION@.0">
    <description>Homogeneity of molecular variance</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 '$dist' dist.dat &&
ln -s '$design' design.dat &&

echo 'homova(
    phylip=dist.dat,
    design=design.dat,
    #if $sets:
        sets=${ str($sets).replace(",","-") },
    #end if
    iters=$iters,
    alpha=$alpha
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
        <param name="design" type="data" format="mothur.design" label="design - assign groups to new grouping" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character)"/>
        <param name="alpha" type="float" optional="true" value="0.05" min="0.0" label="alpha - acceptable stopping precision (default 0.05)"/>
        <param name="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try (default 1000)"/>
        <param name="sets" type="select" multiple="true" label="sets - Which of the sets in your design file you would like to analyze. The set names are separated by dashes. The default is all sets in designfile">
            <options>
                <filter type="data_meta" ref="design" key="groups"/>
            </options>
        </param>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="homova" format="tabular" from_work_dir="dist*.homova" label="${tool.name} on ${on_string}: homova"/>
    </outputs>
    <tests>
        <test><!-- test default settings -->
            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
            <param name="design" value="amazon.design" ftype="tabular"/>
            <output name="homova" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/>
                    <has_text text="A-B"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with subsets -->
            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
            <param name="design" value="amazon.design" ftype="mothur.design"/>
            <param name="sets" value="A"/>
            <output name="homova" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="^HOMOVA\tBValue\tP-value\tSSwithin/\(Ni-1\)_values$"/>
                    <has_line_matching expression="A\t.*$"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The homova_ command calculates the homogeneity of molecular variance (HOMOVA) from a phylip_distance_matrix_, a nonparametric analog of Bartlett's test for homo- geneity of variance, which has been used in population genetics to test the hypothesis that the genetic diversity within two or more populations is homogeneous.

A design file partitions a list of names into groups.  It is a tab-delimited file with 2 columns: name and group, e.g. :
        ======= =======
        duck    bird
        cow     mammal
        pig     mammal
        goose   bird
        cobra   reptile
        ======= =======

The Make_Design tool can construct a design file from a Mothur dataset that contains group names.

.. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _homova: https://www.mothur.org/wiki/Homova

v.1.20.0: Updated to Mothur 1.33, added sets parameter

    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1046/j.1420-9101.1996.9020153.x</citation>
    </expand>
</tool>