<tool profile="16.07" id="mothur_get_dists" name="Get.dists" version="@WRAPPER_VERSION@.0">
    <description>selects distances from a phylip or column file</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 '$accnos' accnos.dat &&
ln -s '$input.dist' input.dist.dat &&

echo 'get.dists(
    accnos=accnos.dat,
    #if $input.source == "phylip":
        phylip=input.dist.dat
    #else
        column=input.dist.dat
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="source" type="select" label="Select input format">
                <option value="column">Pairwise Column Distance Matrix</option>
                <option value="phylip">Phylip Distance Matrix</option>
            </param>
            <when value="column">
                <param name="dist" type="data" format="mothur.pair.dist" label="column - Distance Matrix"/>
            </when>
            <when value="phylip">
                <param name="dist" type="data" format="mothur.dist,mothur.lower.dist,mothur.square.dist" label="phylip - Distance Matrix"/>
            </when>
        </conditional>
        <param name="accnos" type="data" format="mothur.accnos" label="accnos - sort" help="format must be mothur.accnos"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="pick_dist" format_source="dist" from_work_dir="input.dist*.pick.dat" label="${tool.name} on ${on_string}: pick.dist"/>
    </outputs>
    <tests>
        <test>
            <param name="source" value="phylip"/>
            <param name="dist" value="98_sq_phylip_amazon.dist" ftype="mothur.square.dist"/>
            <param name="accnos" value="amazon.bad.accnos" ftype="mothur.accnos"/>
            <output name="pick_dist" md5="d853cca7b67723e889a563420f6ccc13" ftype="mothur.square.dist"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The get.dists_ command selects distances from a phylip or column file related to groups or sequences listed in an accnos file.

.. _get.dists: https://www.mothur.org/wiki/Get.dists

v.1.20.0: Updated to Mothur 1.33

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