<tool id="kobas_identify" name="KOBAS Identify" version="@WRAPPER_VERSION@">
    <description>KEGG Orthology Based Annotation System</description>
    <macros>
        <import>kobas_macros.xml</import>
    </macros>

    <expand macro="requirements"/>

    <command>
        <![CDATA[

        mkdir sqlite &&
        mkdir seq_pep &&

        #if not isinstance( $db.value, list ):
            #set $db_args = [ $db.value ]
        #else:
            #set $db_args = $db.value
        #end if
        #set $db_args = "/".join($db.value)

        ln -s '$kobasdb' 'sqlite/${species}.db' &&

        kobas-identify
            -f '$fgfile'
            #if $bg.bgtype == 'file':
                -b '$bg.bgfile'
            #elif $bg.bgtype == 'species':
                -b '$bg.bgspecies'
            #end if
            -d '$db_args'
            -m '$method'
            -n '$fdr'
            -c $cutoff
            -q sqlite
            -p blastp
            -x blastx
            -o '$output'
        ]]>
    </command>
    <inputs>
        <param format="tabular" type="data" label="Foreground" argument="--fgfile" help="Foreground file, the output of KOBAS Annotate"/>

        <expand macro="input_kobasdb"/>

        <param type="select" label="Database" argument="--db" multiple="True" display="checkboxes" help="Select your desired databases:
(Note: the Corrected P-Values will be affected by the number of selected databases)">
            <option value="K">KEGG Pathway</option>
            <option value="n">PID</option>
            <option value="b">BioCarta</option>
            <option value="R">Reactome</option>
            <option value="B">BioCyc</option>
            <option value="P">PANTHER</option>
            <option value="o">OMIM</option>
            <option value="k">KEGG Disease</option>
            <option value="f">FunDo</option>
            <option value="g">GAD</option>
            <option value="N">NHGRI GWAS Catalog</option>
            <option value="G">Gene Ontology</option>
            <option value="S">Gene Ontology Slim (GOslim)</option>
            <validator type="no_options" message="You must pick at least one database."/>
        </param>

        <conditional name="bg">
            <param
                name="bgtype"
                type="select"
                argument="--bgfile"
                label="Background"
                help="Optional background file, the output of annotate (3 or 4-letter
                        file name is not allowed), or species abbreviation
                        (for example: hsa for Homo sapiens, mmu for Mus
                        musculus, dme for Drosophila melanogaster, ath for
                        Arabidopsis thaliana, sce for Saccharomyces cerevisiae
                        and eco for Escherichia coli K-12 MG1655), default
                        same species as annotate">
                <option value="same" selected="True">Same species as annotate</option>
                <option value="file">Background file from KOBAS Annotate</option>
                <option value="species">Species abbreviation</option>
            </param>
            <when value="same"></when>
            <when value="file">
                <param format="txt" name="bgfile" type="data" label="Background file"/>
            </when>
            <when value="species">
                <param
                    name="bgspecies"
                    type="text"
                    label="Species abbreviation"
                    help="For example: ko for KEGG
                        Orthology, hsa for Homo sapiens, mmu for Mus musculus,
                        dme for Drosophila melanogaster, ath for Arabidopsis
                        thaliana, sce for Saccharomyces cerevisiae and eco for
                        Escherichia coli K-12 MG1655"/>
            </when>
        </conditional>

        <param argument="--method" type="select" label="Statistical test method">
            <option selected="True" value="h">Hpergeometric test / Fisher's exact test</option>
            <option value="b">Binomial test</option>
            <option value="c">Chi-square test</option>
            <option value="x">Frequency list</option>
        </param>

        <param type="select" argument="--fdr" label="FDR" help="False discovery rate (FDR) correction method">
            <option selected="True" value="BH">Benjamini and Hochberg</option>
            <option value="BY">Benjamini and Yekutieli</option>
            <option value="QVALUE">QVALUE</option>
            <option value="None">None</option>
        </param>

        <param type="integer" min="0" argument="--cutoff" value="5" label="Cutoff" help="Terms with less than cutoff number of genes are not used for statistical tests, default 5"/>

    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>

    <tests>
        <test>
            <param name="fgfile" value="kobas_annotate_output.txt"/>
            <param name="species" value="aaa"/>
            <param name="kobasdb" value="aaa.db"/>
            <param name="db" value="K"/>
            <conditional name="bg">
                <param name="bgtype" value="same"/>
            </conditional>
            <output name="out_file1" file="kobas_identify_output.txt"/>
        </test>
    </tests>

    <help>
@HELP_KOBAS_INFO@

**KOBAS Identify**

Performs statistical tests to identify significantly enriched pathways and diseases.

@HELP_KOBAS_URL@
    </help>
    <expand macro="kobas_citations"/>
</tool>