annotate get.sabund.xml @ 2:502c0ba699fb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit 3418f23b9768f5aafb86488f5ec1cb97530d4fb3

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

echo 'get.sabund(
    #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 $otu.is_of_type("mothur.rabund"):
        rabund=otu.dat
    #end if
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list,mothur.rabund" label="list,rabund - List or Rabund"/>
        <param name="label" type="select" optional="true" multiple="true" label="label - select OTU distance labels" help="(all used if none are selected)">
            <expand macro="labeloptions"/>
        </param>
        <param name="count" type="data" format="mothur.count_table" optional="true"
            help="If your list file contains only the unique sequence names because you ran cluster with a count file, be sure to include the count file."/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="sabund" format="mothur.sabund" from_work_dir="otu*.sabund" label="${tool.name} on ${on_string}: sabund (Species Abundance)"/>
    </outputs>
    <tests>
        <test><!-- test rabund input -->
            <param name="otu" value="amazon.an.rabund" ftype="mothur.rabund"/>
            <output name="sabund" file="amazon.an.sabund2" ftype="mothur.sabund"/>
            <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"/>
            <param name="label" value="0.03,0.05"/>
            <output name="sabund" file="amazon.an.sabund3" ftype="mothur.sabund"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@


**Command Documentation**

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

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

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