annotate remove.otus.xml @ 0:4b07bc776ccb draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/mothur commit a9d1e0debcd357d8080a1c6c5f1d206dd45a7a4d

<tool profile="16.07" id="mothur_remove_otus" name="Remove.otus" version="@WRAPPER_VERSION@.0">
    <description>Remove otus containing sequences from specified groups</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 "$otu" otu.dat &&
        ln -s "$group_in" group_in.dat &&

        echo 'remove.otus(
            list=otu.dat,
            label=$label,
            group=group_in.dat
            #if $groups:
                ,groups=${ str($groups).replace(",","-") }
            #end if
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
        <param name="label" type="select" label="label - OTU Labels" help="Select exactly one label">
            <expand macro="labeloptions"/>
        </param>
        <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
        <param name="groups" type="select" label="groups - Pick groups to remove" multiple="true" help="At least one group must be selected">
            <options>
                <filter type="data_meta" ref="group_in" key="groups"/>
            </options>
        </param>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.dat" label="${tool.name} on ${on_string}: pick.groups"/>
        <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.dat" label="${tool.name} on ${on_string}: pick.list"/>
    </outputs>
    <tests>
        <test>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
            <param name="groups" value="forest"/>
            <param name="label" value="0.05"/>
            <output name="list_out" md5="fa5b954ad8e8235dbb700af1a9d8a091" ftype="mothur.list"/>
            <output name="group_out" md5="3c9f6e88de0f60f2a870c8d4a9d61db8" ftype="mothur.groups"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The remove.otus_ command removes otus from a list_ containing sequences from a specific group or set of groups.

.. _list: https://www.mothur.org/wiki/List_file
.. _remove.otus: https://www.mothur.org/wiki/Remove.otus

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