view get.group.xml @ 6:081d0fbf9751 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit debdcdbb89f9bf3e2c3eed05cb078eddb27d4684"

<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 '$shared' shared.dat &&

echo 'get.group(
    shared=shared.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 '1,30d'
> "$bootgroups"
    ]]></command>
    <inputs>
        <param argument="shared" type="data" format="mothur.shared" label="shared - OTU Shared"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="bootgroups" format="mothur.groups" label="${tool.name} on ${on_string}: bootGroups"/>
    </outputs>
    <tests>
        <test>
            <param name="shared" value="amazon.an.shared" ftype="mothur.shared"/>
            <output name="bootgroups" md5="93b9f7ead2ee04f056e77b5bb94ea0dd"/>
            <param name="savelog" value="true"/>
            <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>