<commit_before><tool profile="16.07" id="mothur_anosim" name="Anosim" version="@WRAPPER_VERSION@.0">
    <description>Non-parametric multivariate analysis of changes in community structure</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 '$phylip' phylip.dat &&
ln -s '$design' design.dat &&

echo 'anosim(
    phylip=phylip.dat,
    iters=$iters,
    alpha=$alpha,
    design=design.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
        <param argument="design" type="data" format="tabular" 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 argument="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision" help="default: 0.05"/>
        <param argument="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try" help="default: 1000"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="anosim" format="tabular" from_work_dir="phylip.anosim" label="${tool.name} on ${on_string}: anosim"/>
    </outputs>
    <tests>
        <test>
            <param name="phylip" value="amazon.dist"/>
            <param name="design" value="amazon.design"/>
            <output name="anosim" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="^comparison\tR-value\tP-value$"/>
                    <has_line_matching expression="^A-B\t[0-9\.\-]+\t[0-9\.]+$"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The anosim_ command uses a phylip_distance_matrix_ and a design file to calculate the non-parametric multivariate analysis of changes in community structure.

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
.. _anosim: https://www.mothur.org/wiki/Anosim

    ]]></help>
    <expand macro="citations"/>
</tool><commit_msg>anosimw: add citation<commit_after><tool profile="16.07" id="mothur_anosim" name="Anosim" version="@WRAPPER_VERSION@.0">
    <description>Non-parametric multivariate analysis of changes in community structure</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 '$phylip' phylip.dat &&
ln -s '$design' design.dat &&

echo 'anosim(
    phylip=phylip.dat,
    iters=$iters,
    alpha=$alpha,
    design=design.dat
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param argument="phylip" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
        <param argument="design" type="data" format="tabular" 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 argument="alpha" type="float" optional="true" value="0.05" min="0" label="alpha - acceptable stopping precision" help="default: 0.05"/>
        <param argument="iters" type="integer" value="1000" min="0" label="iters - Number of random configuration to try" help="default: 1000"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="anosim" format="tabular" from_work_dir="phylip.anosim" label="${tool.name} on ${on_string}: anosim"/>
    </outputs>
    <tests>
        <test>
            <param name="phylip" value="amazon.dist"/>
            <param name="design" value="amazon.design"/>
            <output name="anosim" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="^comparison\tR-value\tP-value$"/>
                    <has_line_matching expression="^A-B\t[0-9\.\-]+\t[0-9\.]+$"/>
                </assert_contents>
            </output>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The anosim_ command uses a phylip_distance_matrix_ and a design file to calculate the non-parametric multivariate analysis of changes in community structure.

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
.. _anosim: https://www.mothur.org/wiki/Anosim

    ]]></help>
    <expand macro="citations">
        <citation type="doi">10.1111/j.1442-9993.1993.tb00438.x</citation>
    </expand>
</tool>
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