<tool profile="16.07" id="mothur_get_otus" name="Get.otus" version="@WRAPPER_VERSION@.0">
    <description>Get 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 &&
        #if $groupnames.source == 'accnos':
            ln -s "$groupnames.accnos_in" groupnames.accnos_in.dat &&
        #end if

        echo 'get.otus(
            list=otu.dat,
            group=group_in.dat
            #if $label:
                ,label=${ str($label).replace(",","-") }
            #end if
            #if $groupnames.source == 'groups':
                ,groups=${ str($groupnames.groups).replace(",","-") }
            #else
                ,accnos=groupnames.accnos_in.dat
            #end if
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.list" label="list - OTU List"/>
        <param name="label" type="select" optional="true" multiple="false" label="label - OTU Label" help="select exactly one label. If none selected, the first label in your file will be used">
            <expand macro="labeloptions"/>
        </param>
        <param name="group_in" type="data" format="mothur.groups" label="group - Groups"/>
        <conditional name="groupnames">
            <param name="source" type="select" label="Select Group Names from">
                <option value="groups">A List of Group Names</option>
                <option value="accnos">A History Group Name Accnos Dataset</option>
            </param>
            <when value="groups">
                <param name="groups" type="select" multiple="true" force_select="true" label="groups - Pick groups to include">
                    <help>At least one group must be selected</help>
                    <options>
                        <filter type="data_meta" ref="group_in" key="groups"/>
                    </options>
                </param>
            </when>
            <when value="accnos">
                <param name="accnos_in" type="data" format="mothur.accnos" optional="true" label="accnos - Group Names from your history"/>
            </when>
        </conditional>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="group_out" format="mothur.groups" from_work_dir="group_in*.pick.*" label="${tool.name} on ${on_string}: pick.groups"/>
        <data name="list_out" format="mothur.list" from_work_dir="otu*.pick.*" label="${tool.name} on ${on_string}: pick.list"/>
    </outputs>
    <tests>
        <test><!-- test with group file -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
            <param name="source" value="groups"/>
            <param name="groups" value="forest,pasture"/>
            <output name="list_out" md5="a771e0879bbb84e2764db70f66ae1277" ftype="mothur.list"/>
            <output name="group_out" md5="954ef97da9dcd152b912bcda19a6f96c" ftype="mothur.groups"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with accnos file and label select -->
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="label" value="0.03"/>
            <param name="group_in" value="amazon.groups" ftype="mothur.groups"/>
            <param name="source" value="accnos"/>
            <param name="accnos_in" value="amazon.groupaccnos" ftype="mothur.accnos"/>
            <output name="list_out" md5="2069739b1f7bbbe47cc237833450e57c" ftype="mothur.list"/>
            <output name="group_out" md5="09ffabe975dc49f1bf251ea60c569526" ftype="mothur.groups"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help>
<![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

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

.. _list: https://www.mothur.org/wiki/List_file
.. _get.otus: https://www.mothur.org/wiki/Get.otus

v.1.20.0: Updated to Mothur 1.33
]]>
    </help>
    <expand macro="citations"/>
</tool>