<macros>
    <token name="@TOOL_VERSION@">2.1.1</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">kobas</requirement>
            <!-- kobas 2.1.1 is not compatible with Biopython >=1.73 due to https://github.com/biopython/biopython/issues/1952 -->
            <requirement type="package" version="1.72">biopython</requirement>
            <!-- Help conda resolving the enviroment, hopefully this can be removed for next update -->
            <requirement type="package" version="3.4">r-base</requirement>
        </requirements>
    </xml>
    <xml name="input_kobasdb">
        <param argument="--species" 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"/>
        <param name="kobasdb" type="data" format="sqlite" label="KOBAS database" help="KOBAS species database, available for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/>
    </xml>
    <xml name="blastdb_selector">
        <param name="choice" type="select" label="BLAST Protein database">
            <option value="histdb">BLAST database from your history</option>
            <option value="fasta">BLAST database from FASTA File</option>
            <option value="local" selected="True">Locally installed BLAST database</option>
        </param>
        <when value="fasta">
            <param name="fastadb" type="data" format="fasta" label="FASTA File for BLAST DB" help="FASTA file which will be used to create a BLAST database with makeblastdb."/>
        </when>
        <when value="histdb">
            <param name="histdb" type="data" format="blastdbp" label="Protein BLAST database"
                help="The protein BlAST database used by KOBAS. FASTA files to create BLAST databases with makeblastdb can be found for multiple species at http://kobas.cbi.pku.edu.cn/download.php"/>
        </when>
        <when value="local">
            <param name="localdb" type="select" label="Protein BLAST database">
                <options from_data_table="blastdb_p"/>
            </param>
        </when>
    </xml>
    <xml name="kobas_citations">
        <citations>
            <citation type="doi">10.1093/nar/gkr483</citation>
        </citations>
    </xml>

    <token name="@HELP_KOBAS_INFO@">
**KOBAS**

KOBAS is a KEGG Orthology Based Annotation System. Its purpose is to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. The necessary KOBAS databases for multiple species can be downloaded from http://kobas.cbi.pku.edu.cn/download.php
    </token>
    <token name="@HELP_KOBAS_URL@">
        KOBAS can be accessed at http://kobas.cbi.pku.edu.cn
    </token>
</macros>