view get.group.xml @ 0:200b088eaf93 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

<tool profile="16.07" id="mothur_get_group" name="Get.group" version="@WRAPPER_VERSION@.0">
    <description>group names from shared or from list and group</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.group(
            shared=otu.dat
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log &&

        ## parse relevant output from logfile to file
        cat mothur.*.logfile
        | head -n-6
        | sed '1,29d'
        > "$bootgroups"
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="bootgroups" format="mothur.groups" label="${tool.name} on ${on_string}: bootGroups"/>
    </outputs>
    <tests>
        <test>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output name="bootgroups" md5="93b9f7ead2ee04f056e77b5bb94ea0dd"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The get.group_ command generate principle components plot data.

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

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