<tool profile="16.07" id="mothur_sens_spec" name="Sens.spec" version="@WRAPPER_VERSION@.0">
    <description>Determine the quality of OTU assignment</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 "$otu" otu.dat &&
        ln -s "$dist" dist.dat &&

        echo 'sens.spec(
            list=otu.dat,
            #if $dist.is_of_type("mothur.dist"):
                column=dist.dat,
            #else
                phylip=dist.dat,
            #end if
            #if $label:
                label=${ str($label).replace(",","-") },
            #end if
            precision=$precision,
            cutoff=$cutoff,
            hard=$hard
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
        <param name="dist" type="data" format="mothur.dist,phylip,tabular" label="phylip,column - Distance Matrix"/>
        <param name="label" type="select" optional="true" label="label - Select OTU Labels to include" multiple="true" help="By default all are included if no selection is made.">
            <options>
                <filter type="data_meta" ref="otu" key="labels"/>
            </options>
        </param>
        <param name="precision" type="integer" value="100" min="0" optional="true" label="precision - Precision for rounding distance values"/>
        <param name="cutoff" type="float" value="-1" label="cutoff - Distance Cutoff threshold - ignored if not > 0" help="Ignore pairwise distances larger than this, a common value would be 0.10"/>
        <param name="hard" type="boolean" checked="false" truevalue="true" falsevalue="false" label="hard - Use hard cutoff instead of rounding"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="sensspec" format="tabular" from_work_dir="otu*.sensspec" label="${tool.name} on ${on_string}: sensspec"/>
    </outputs>
    <tests>
        <test>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
            <output name="sensspec" md5="5eb92a89c4e1fd78c10e5bbe55ee2a7a" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="dist" value="amazon.dist" ftype="mothur.dist"/>
            <param name="cutoff" value="0.10"/>
            <param name="label" value="0.03,0.05,0.22"/>
            <output name="sensspec" md5="8e2f46ef59b1ac097a9de2e0ab669bb2" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The sens.spec_ command takes a list_ and either a column_  or phylip_ distance matrix to determine the quality of OTU assignment.


.. _list: https://www.mothur.org/wiki/List_file
.. _column: https://www.mothur.org/wiki/Column-formatted_distance_matrix
.. _phylip: https://www.mothur.org/wiki/Phylip-formatted_distance_matrix
.. _sens.spec: https://www.mothur.org/wiki/Sens.spec
]]>
    </help>
    <expand macro="citations"/>
</tool>