annotate get.label.xml @ 9:07d9a6a72e6d draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 4c950508328589b5215b6c96868659a03f9dead8"

<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 '1,30d'
> '$labels_list'
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list,mothur.sabund,mothur.rabund" label="Input file. May be shared, sabund or rabund file"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="labels_list" format="tabular" label="${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"/>
            <param name="savelog" value="true"/>
            <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"/>
            <param name="savelog" value="true"/>
            <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"/>
            <param name="savelog" value="true"/>
            <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>