annotate list.otulabels.xml @ 6:e643cc6c39cb draft

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

<tool profile="16.07" id="mothur_list_otulabels" name="List.otulabels" version="@WRAPPER_VERSION@.0">
    <description>Lists otu labels from shared or relabund 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 'list.otulabels(
    #if $otu.is_of_type("mothur.relabund"):
        relabund=otu.dat
    #elif $otu.is_of_type("mothur.shared"):
        shared=otu.dat
    #else
        list=otu.dat
    #end if
    #if $label:
        ,label=${ str($label).replace(",","-") }
    #end if
    #if $groups:
        ,groups=${ str($groups).replace(",","-") }
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared,mothur.relabund,mothur.list" label="list or shared or relabund - OTU List or Shared or Relabund"/>
        <param name="label" type="select" multiple="true" label="label - OTU Labels">
            <expand macro="labeloptions"/>
        </param>
        <param name="groups" type="select" multiple="true" label="groups - Pairwise comparision groups">
            <options>
                <filter type="data_meta" ref="otu" key="groups"/>
            </options>
        </param>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <collection name="otulabels" type="list" label="${tool.name} on ${on_string}: otulabels">
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.otulabels" format="mothur.otulabels"/>
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="infile" value="otulist"/>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <output_collection name="otulabels" count="36">
                <element name="unique" md5="c901cebfbc87559f1667546111408a22" ftype="mothur.otulabels"/>
                <element name="0.55" md5="0e0dcf8a91c03e1cc6adbf2593addf20" ftype="mothur.otulabels"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with group select -->
            <param name="infile" value="otulist"/>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="groups" value="forest"/>
            <output_collection name="otulabels" count="36">
                <element name="unique" md5="8a4d85496fdcfdf99337129989350e7e" ftype="mothur.otulabels"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The list.otulabels_ command lists otu labels from shared_ or relabund_ file. This list can be used especially with subsampled datasets when used with output from classify.otu_, otu.association_, or corr.axes_ to select specific otus using the get.otus_ or remove.otulabels_ commands

.. _list.otulabels: https://www.mothur.org/wiki/List.otulabels
.. _classify.otu: https://www.mothur.org/wiki/Classify.otu
.. _otu.association: https://www.mothur.org/wiki/Otu.association
.. _corr.axes: https://www.mothur.org/wiki/Corr.axes
.. _get.otus: https://www.mothur.org/wiki/Get.otus
.. _remove.otulabels: https://mothur.org/wiki/Remove.otus
.. _shared: https://www.mothur.org/wiki/Shared_file
.. _relabund: https://www.mothur.org/wiki/Get.relabund

v.1.27.0: Updated to mothur 1.33, added list file for otu

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