<tool profile="16.07" id="mothur_get_label" name="Get.label" version="@WRAPPER_VERSION@.0">
    <description>label names from list, sabund, or rabund 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 "$otu" otu.dat &&

        echo 'get.label(
            #if $otu.is_of_type("mothur.rabund"):
                rabund=otu.dat
            #elif $otu.is_of_type("mothur.sabund"):
                sabund=otu.dat
            #else
                list=otu.dat
            #end if
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log &&

        ## parse relevant output from logfile to file
        cat mothur.*.logfile
        | head -n-3
        | sed '1,29d'
        > "$labels_list"
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list,motur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="labels_list" format="tabular" label="${tool.name} on ${on_string}: labels"/>
    </outputs>
    <tests>
        <test><!-- test with sabund -->
            <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
            <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with rabund -->
            <param name="otu" value="amazon.an.rabund2" ftype="mothur.rabund"/>
            <output name="labels_list" md5="0c3fab5bdfa8588c7244048ddd4eac3c" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with list -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <output name="labels_list" md5="ded659c0af6b78f710f53f45ea99b9bb" ftype="tabular"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The get.label_ command generate principle components plot data.

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

v.1.20.0: Updated to Mothur 1.33
]]>
    </help>
    <expand macro="citations"/>
</tool>