annotate get.relabund.xml @ 1:e034a3d4b6c7 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 721531d2e9fd1e208a3fba8cfbe5dcd572599ca2

<tool profile="16.07" id="mothur_get_relabund" name="Get.relabund" version="@WRAPPER_VERSION@.0">
    <description>Calculate the relative abundance of each otu</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.relabund(
            shared=otu.dat,
            #if $label:
                label=${ str($label).replace(",","-") },
            #end if
            #if $groups:
                groups=${ str($groups).replace(",","-") },
            #end if
            scale=$scale
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared" help="Use Make.shared to create a shared file from a list and a group file"/>
        <param name="label" type="select" label="label - OTU Labels" multiple="true">
            <expand macro="labeloptions"/>
        </param>
        <param name="groups" type="select"  multiple="true" label="groups - Groups to consider">
            <options>
                <filter type="data_meta" ref="otu" key="groups"/>
            </options>
        </param>
        <param name="scale" type="select" label="scale - Scale by">
            <option value="totalgroup" selected="true">Total Groups</option>
            <option value="totalotu">Total OTUs</option>
            <option value="averagegroup">Average Groups</option>
            <option value="averageotu">Average OTUs</option>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="relabund" format="mothur.relabund" from_work_dir="otu*.relabund" label="${tool.name} on ${on_string}: relabund"/>
    </outputs>
    <tests>
        <test>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output name="relabund" file="amazon.an.relabund" ftype="mothur.relabund"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="label" value="0.03,0.05,0.22"/>
            <param name="groups" value="forest"/>
            <output name="relabund" md5="3f91820ebdf2d4c640b7d1489fd67936" ftype="mothur.relabund"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The get.relabund_ command calculates the relative abundance of each otu in a sample from a shared_ file. It outputs a .relabund_ file.

.. _shared: https://www.mothur.org/wiki/Shared_file
.. _get.relabund: https://www.mothur.org/wiki/Get.relabund

v.1.21.0: Updated to Mothur 1.33
]]>
    </help>
    <expand macro="citations"/>
</tool>