<tool profile="16.07" id="mothur_classify_rf" name="Classify.rf" version="@WRAPPER_VERSION@.0">
    <description>description</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 '$otu' shared.dat &&
        ln -s '$design' design.dat &&

        echo 'classify.rf(
            shared=shared.dat,
            design=design.dat
            #if $label:
                ,label=${ str($label).replace(",","-") }
            #end if
            #if $groups:
                ,groups=${ str($groups).replace(",","-") }
            #end if
            #if $otupersplit:
                ,otupersplit=$otupersplit
            #end if
            #if $seed:
                ,seed=$seed
            #end if
        )'
        | sed 's/ //g'  ## mothur trips over whitespace
        | mothur
        | tee mothur.out.log
    ]]></command>
    <inputs>
        <param name="otu" type="data" format="mothur.shared" label="shared - OTU Shared"/>
        <param name="design" type="data" format="mothur.design" label="design - assigns groups to sets" help="design has 2 columns: group(col 1) and grouping(col 2) (separated by a TAB character) use make.design"/>
        <param name="label" type="select" multiple="true" optional="true" label="label - OTU Label filter">
            <expand macro="labeloptions"/>
        </param>
        <param name="groups" type="select" multiple="true" optional="true" label="groups - Groups filter (uses all groups if none are selected)" help="To filter: select select at least 2 groups">
            <options>
                <filter type="data_meta" ref="otu" key="groups"/>
            </options>
        </param>
        <param name="otupersplit" type="select" optional="true" label="otupersplit">
            <option value="log2">log2</option>
            <option value="squareroot">square root</option>
        </param>
        <param name="seed" type="integer" value="" min="0" optional="true" label="seed" help="Will be randomly chosen if left blank"/>
    </inputs>
    <outputs>
        <expand macro="logfile-output"/>
        <data name="summary" format="tabular" from_work_dir="shared.RF*summary" label="${tool.name} on ${on_string}: summary"/>
        <data name="misclass-summary" format="tabular" from_work_dir="shared.misclassifications*.summary" label="${tool.name} on ${on_string}: misclassifications summary"/>
    </outputs>
    <tests>
        <test><!-- test with defaults -->
            <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
            <param name="design" value="mouse.design"/>
            <output name="summary" md5="dd5501c82a66b681b6b9961bcf731d7d" ftype="tabular"/>
            <output name="misclass-summary" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="Sample\tRF classification\tActual classification"/>
                    <has_text text="F003D000"/>
                    <has_text text="F003D150"/>
                </assert_contents>
            </output>
            <expand macro="logfile-test"/>
        </test>
        <test><!-- test with custom settings -->
            <param name="otu" value="final.tx.1.subsample.1.pick.shared" ftype="mothur.shared"/>
            <param name="design" value="mouse.design"/>
            <param name="label" value="1"/>
            <param name="otupersplit" value="log2"/>
            <param name="groups" value="F003D000,F003D002,F003D006,F003D008,F003D142,F003D144,F003D146,F003D148"/>
            <param name="seed" value="42"/> <!-- tool will unpredictable segfault without this -->
            <output name="summary" md5="dd5501c82a66b681b6b9961bcf731d7d" ftype="tabular"/>
            <output name="misclass-summary" ftype="tabular">
                <assert_contents>
                    <has_line_matching expression="Sample\tRF classification\tActual classification"/>
                    <has_text text="F003D000"/>
                    <not_has_text text="F003D150"/>
                </assert_contents>
            </output>
            <expand macro="logfile-test"/>
        </test>
    </tests>
    <help><![CDATA[
@MOTHUR_OVERVIEW@


**Command Documentation**


.. _classify.rf: https://www.mothur.org/wiki/Classify.rf
    ]]></help>
    <expand macro="citations"/>
</tool>