<tool profile="16.07" id="mothur_remove_rare" name="Remove.rare" version="@WRAPPER_VERSION@.0">
    <description>Remove rare OTUs</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 '$input.otu' input_otu.dat &&
#if $input.source == 'list':
    ln -s '$input.group' input.group.dat &&
    ln -s '$input.count' input.count.dat &&
#end if

echo 'remove.rare(
    #if $input.otu.is_of_type("mothur.rabund"):
        rabund=input_otu.dat,
    #elif $input.otu.is_of_type("mothur.sabund"):
        sabund=input_otu.dat,
    #elif $input.otu.is_of_type("mothur.list"):
        list=input_otu.dat,
        #if $input.group:
            group=input.group.dat,
        #end if
        #if $input.groups:
            groups=${ str($input.groups).replace(",","-") },
        #end if
        #if $input.count:
            count=input.count.dat,
        #end if
    #elif $input.otu.is_of_type("mothur.shared"):
        shared=input_otu.dat,
        bygroup=$input.bygroup,
        #if $input.groups:
            groups=${ str($input.groups).replace(",","-") },
        #end if
    #end if
    #if $input.label:
        label=${ str($input.label).replace(",","-") },
    #end if
    nseqs=$nseqs
)'
| sed 's/ //g'  ## mothur trips over whitespace
| mothur
| tee mothur.out.log
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="source" type="select" label="Select Input Format">
                <option value="shared">shared</option>
                <option value="list">list</option>
                <option value="default">rabund or sabund</option>
            </param>
            <when value="shared">
                <param name="otu" type="data" format="mothur.shared" label="shared - Otu dataset"/>
                <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
                    <options>
                        <filter type="data_meta" ref="otu" key="groups"/>
                    </options>
                </param>
                <param name="bygroup" type="boolean" truevalue="true" falsevalue="false" checked="false" label="bygroup - Remove any OTU that has nseqs or fewer sequences across all groups"/>
                <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels">
                    <expand macro="labeloptions"/>
                </param>
            </when>
            <when value="list">
                <param name="otu" type="data" format="mothur.list" label="list - Otu dataset"/>
                <param name="group" type="data" optional="true" format="mothur.groups" label="group - Groups"/>
                <param name="count" type="data" format="mothur.count_table" optional="true" label="count - Count Table" help="If you clustered with a count file, can only supply one of group or count table, not both"/>
                <param name="groups" type="select" optional="true" label="groups - Pick groups to analyze" multiple="true">
                    <options>
                        <filter type="data_meta" ref="group" key="groups"/>
                    </options>
                </param>
                <param name="label" type="select" multiple="false" optional="true" label="label - OTU Labels">
                    <expand macro="labeloptions"/>
                </param>
            </when>
            <when value="default">
                <param name="otu" type="data" format="mothur.list,mothur.rabund,mothur.sabund" label="list,rabund,sabund - Otu dataset"/>
                <param name="label" type="select" multiple="true" optional="true" label="label - OTU Labels">
                    <expand macro="labeloptions"/>
                </param>
            </when>
        </conditional>
        <param name="nseqs" type="integer" value="1" min="0" label="nseqs - Number of sequences cutoff for an otu to be deemed rare"/>
        <expand macro="param-savelog"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="pick_otu" format_source="otu" from_work_dir="input_otu*.pick.*" label="${tool.name} on ${on_string}: pick.${input.otu.ext}">
            <filter>input['source'] != 'shared'</filter>
        </data>
        <collection name="pick_shared" type="list" label="${tool.name} on ${on_string}: pick.shared per label">
            <filter>input['source'] == 'shared'</filter>
            <discover_datasets pattern=".*?\.(?P&lt;designation&gt;.*)\.pick\.dat" format="mothur.shared"/>
        </collection>
        <data name="pick_group" format="mothur.groups" from_work_dir="input.group*.pick.*" label="${tool.name} on ${on_string}: pick.groups">
            <filter>input['source'] == 'list'</filter>
        </data>
    </outputs>
    <tests>
        <test><!-- test with list -->
            <param name="source" value="list"/>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with list and group file -->
            <param name="source" value="list"/>
            <param name="otu" value="amazon.an.list" ftype="mothur.list"/>
            <param name="group" value="amazon.groups" ftype="mothur.groups"/>
            <param name="groups" value="forest,pasture"/>
            <output name="pick_otu" md5="4779791c9b0ef95a54083ee1a6ad6c8d" ftype="mothur.list"/>
            <output name="pick_group" md5="9561ba470c769670ab6d92563a44027f" ftype="mothur.groups"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with shared file -->
            <param name="source" value="shared"/>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <output_collection name="pick_shared" count="36">
                <element name="0.38" md5="e58da633dd16f0cb6472d6c6b3318c9f" ftype="mothur.shared"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with shared file and label/group select -->
            <param name="source" value="shared"/>
            <param name="otu" value="amazon.an.shared" ftype="mothur.shared"/>
            <param name="bygroup" value="true"/>
            <param name="label" value="0.05,0.22,0.41"/>
            <param name="groups" value="forest,pasture"/>
            <output_collection name="pick_shared" count="3">
                <element name="0.22" md5="46d97e6f97e7909d72d09a1726655539" ftype="mothur.shared"/>
            </output_collection>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with rabund/sabund file -->
            <param name="source" value="default"/>
            <param name="otu" value="amazon.an.sabund" ftype="mothur.sabund"/>
            <output name="pick_otu" md5="ca842ed3ef543d3dd76fd9089cd87c46" ftype="mothur.sabund"/>
            <param name="savelog" value="true"/>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[

@MOTHUR_OVERVIEW@

**Command Documentation**

The remove.rare_ command reads one of the following file types: list_, rabund_, sabund_ or shared_ file. It outputs a new file after removing the rare otus.

.. _list: https://www.mothur.org/wiki/List_file
.. _sabund: https://www.mothur.org/wiki/Sabund_file
.. _rabund: https://www.mothur.org/wiki/Rabund_file
.. _shared: https://www.mothur.org/wiki/Shared_file
.. _remove.rare: https://www.mothur.org/wiki/Remove.rare

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