<tool profile="16.07" id="mothur_nmds" name="Nmds" version="@WRAPPER_VERSION@.0">
    <description>generate non-metric multidimensional scaling data</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 '$dist' dist.dat &&
ln -s '$axes' axes.dat &&

echo 'nmds(
    phylip=dist.dat
    #if $axes:
        ,axes=axes.dat
    #end if
    ,mindim=$mindim
    #if $maxdim >= $mindim:
        ,maxdim=$maxdim
    #end if
    ,iters=$iters
    ,maxiters=$maxiters

    ## Mothur can't cope with scientific notation
    #set epsilon_decimal = "{:.12f}".format(float($epsilon))
    ,epsilon=$epsilon_decimal
)'
| 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="axes" type="data" format="mothur.axes" optional="true" label="axes - a starting configuration"/>
        <param name="mindim" type="integer" value="2" min="1" label="mindim - minimum dimensions (default 2)"/>
        <param name="maxdim" type="integer" value="2" label="maxdim - maximum dimensions (default 2)"/>
        <param name="iters" type="integer" value="10" min="1" label="iters - Number of random configuration to try (default 10)"/>
        <param name="maxiters" type="integer" value="500" min="1" label="maxiters - Number of iterations to try with each random configuration (default 500)"/>
        <param name="epsilon" type="float" optional="true" min="0" value="1e-12" label="epsilon - acceptable stopping precision (default 1e-12)"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="nmds_axes" format="mothur.axes" from_work_dir="dist*.axes" label="${tool.name} on ${on_string}: nmds.axes"/>
        <data name="nmds_iters" format="tabular" from_work_dir="dist*.iters" label="${tool.name} on ${on_string}: nmds.iters"/>
        <data name="nmds_stress" format="tabular" from_work_dir="dist*.stress" label="${tool.name} on ${on_string}: nmds.stress"/>
    </outputs>
    <tests>
        <test>
            <param name="dist" value="amazon.dist"/>
            <param name="axes" value="amazon.pcoa.axes"/>
            <param name="mindim" value="1"/>
            <param name="maxdim" value="2"/>
            <param name="iters" value="10"/>
            <param name="maxiters" value="500"/>
            <param name="epsilon" value="1e-12"/>
            <output name="nmds_axes" md5="9a8a5605d9a619ae1c4973a45e963032"/>
            <output name="nmds_iters" md5="979702f1c719dac6a7276adf8363a688"/>
            <output name="nmds_stress" md5="0b46f64bea0294f2c966d7dc890e9aea"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

.. _Mothur: https://www.mothur.org/wiki/Main_Page

**Command Documentation**

The nmds_ command generates non-metric multidimensional scaling data from a phylip_distance_matrix_.

.. _phylip_distance_matrix: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _nmds: https://www.mothur.org/wiki/Nmds

v1.20.0: Updated to mothur 1.33

    ]]></help>
    <expand macro="citations">
        <citation type="bibtex">
@book{cox2000multidimensional,
  title={Multidimensional scaling},
  author={Cox, Trevor F and Cox, Michael AA},
  year={2000},
  publisher={Chapman and hall/CRC}
}
        </citation>
    </expand>
</tool>