annotate phylotype.xml @ 10:e6ecdb693d0c draft default tip

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 7599ef16dc8b83ee49236ed5bb229260c969b0ab

<tool profile="16.07" id="mothur_phylotype" name="Phylotype" version="@WRAPPER_VERSION@.0">
    <description>Assign sequences to OTUs based on taxonomy</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="biotools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <expand macro="version_command"/>
    <command><![CDATA[
@SHELL_OPTIONS@

## create symlinks to input datasets
ln -s '$taxonomy' taxonomy.dat &&
ln -s '$name' name.dat &&

echo 'phylotype(
    taxonomy=taxonomy.dat
    #if $cutoff:
        ,cutoff=$cutoff
    #end if
    #if $name:
        ,name=name.dat
    #end if
    #if $label:
        ,label=${ str($label).replace(",","-") }
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="taxonomy" type="data" format="mothur.seq.taxonomy" label="taxonomy - Taxonomy"/>
        <param name="name" type="data" format="mothur.names" optional="true" label="name - Names reference file for the taxonomy"/>
        <param name="label" type="select" label="label - Taxonomy Levels to report (All when none are selected)" multiple="true">
            <option value="0">0</option>
            <option value="1">1</option>
            <option value="2">2</option>
            <option value="3">3</option>
            <option value="4">4</option>
            <option value="5">5</option>
            <option value="6">6</option>
            <option value="7">7</option>
            <option value="8">8</option>
            <option value="9">9</option>
            <option value="10">10</option>
        </param>
        <param name="cutoff" type="integer" value="" min="0" max="50" optional="true" label="cutoff - Truncate the taxonomy at depth (Ignored if &lt; 0)"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="rabund" format="mothur.rabund" from_work_dir="taxonomy*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
        <data name="sabund" format="mothur.sabund" from_work_dir="taxonomy*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
        <data name="otulist" format="mothur.list" from_work_dir="taxonomy*.list" label="${tool.name} on ${on_string}: list (OTU List)"/>
    </outputs>
    <tests>
        <test>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <output name="rabund" md5="689fb6fd2fb4cd0740fc8b62d7e05556" ftype="mothur.rabund"/>
            <output name="sabund" md5="62547e84f1d051a16937715433f3d78a" ftype="mothur.sabund"/>
            <output name="otulist" md5="c808112d524863bbc973dd721ba18a06" ftype="mothur.list"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test>
            <param name="taxonomy" value="abrecovery.pds.wang.taxonomy" ftype="mothur.seq.taxonomy"/>
            <param name="label" value="1,4,5"/>
            <param name="cutoff" value="5"/>
            <output name="rabund" md5="3d2e3821bef6ecd7eaf0ea62e8692154" ftype="mothur.rabund"/>
            <output name="sabund" md5="582825c475bffbf7e450156ff26c844a" ftype="mothur.sabund"/>
            <output name="otulist" md5="424a2c62df2e37b32542731b9631f8ed" ftype="mothur.list"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The phylotype_ command assign sequences to OTUs based on their taxonomy and outputs a a list_, a sabund_ (Species Abundance), and a rabund_ (Relative Abundance) file.

.. _list: https://www.mothur.org/wiki/List_file
.. _rabund: https://www.mothur.org/wiki/Rabund_file
.. _sabund: https://www.mothur.org/wiki/Sabund_file
.. _phylotype: https://www.mothur.org/wiki/Phylotype

    ]]></help>
    <expand macro="citations"/>
</tool>