annotate get.rabund.xml @ 6:bd695645069f draft

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

<tool profile="16.07" id="mothur_get_rabund" name="Get.rabund" version="@WRAPPER_VERSION@.0">
    <description>Get rabund from a otu list or sabund</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 '$count' count.dat &&
ln -s '$otu' otu.dat &&

echo 'get.rabund(
    #if $label:
        label=${ str($label).replace(",","-") },
    #end if
    #if $count:
        count=count.dat,
    #end if
    #if $otu.is_of_type("mothur.list"):
        list=otu.dat,
    #elif $otu.is_of_type("mothur.sabund"):
        sabund=otu.dat,
    #end if
    sorted=$sorted
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list,mothur.sabund" label="list,sabund - List or Sabund"/>
        <param name="label" type="select" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
            <expand macro="labeloptions"/>
        </param>
        <param name="sorted" type="boolean" checked="false" truevalue="true" falsevalue="false" label="sorted - sort by abundance"
            help="By default the data in the rabund file the same order as the OTUs in input, select to sort by abundance."/>
        <param name="count" type="data" format="mothur.count_table" optional="true" label="count - a count_table" help="generated by count.seqs"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="rabund" format="mothur.rabund" from_work_dir="otu*.rabund" label="${tool.name} on ${on_string}: rabund (Rank Abundance)"/>
    </outputs>
    <tests>
        <test><!-- test sabund input -->
            <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
            <param name="label" value="0.03,0.05"/>
            <output name="rabund" file="amazon.an.rabund2" ftype="mothur.rabund"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test otu list input -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <output name="rabund" file="amazon.an.rabund" ftype="mothur.rabund"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The get.rabund_ command generates an rabund_ file from a list_ or sabund_ file.

.. _rabund: https://www.mothur.org/wiki/Rabund_file
.. _list: https://www.mothur.org/wiki/List_file
.. _sabund: https://www.mothur.org/wiki/Sabund_file
.. _get.rabund: https://www.mothur.org/wiki/Get.rabund

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