<tool id="kobas_annotate" name="KOBAS Annotate" version="@WRAPPER_VERSION@">
    <description>KEGG Orthology Based Annotation System</description>
    <macros>
        <import>kobas_macros.xml</import>
    </macros>
    <requirements>
        <requirement type="package" version="@KOBAS_VERSION@">kobas</requirement>
    </requirements>
    <stdio>
        <exit_code range="0" level="warning" description="BiopythonDeprecationWarning"/>
        <exit_code range="1" level="fatal" description="Bad input settings or none of the entries was annotated successfully."/>
    </stdio>
    <command>
        <![CDATA[

        ## create the KOBAS directories
        mkdir sqlite &&
        mkdir seq_pep &&

        #if $blast_opts.choice == 'local':
            #set $blast_path = $blast_opts.localdb.fields.path
        #else if $blast_opts.choice == 'fasta':
            makeblastdb
                -in '$blast_opts.fastadb'
                -dbtype 'prot'
                -out 'seq_pep/${species}.pep.fasta' &&
        #else:
            #set $blast_path = $os.path.join($blast_opts.histdb.extra_files_path,'blastdb')
        #end if

        ## create the database symlinks to comply with how KOBAS wants them
        ln -s '$organismdb' sqlite/organism.db &&
        ln -s '$kobasdb' 'sqlite/${species}.db' &&

        #if $blast_opts.choice != 'fasta':
            ln -s '${blast_path}.phr' 'seq_pep/${species}.pep.fasta.phr' &&
            ln -s '${blast_path}.pin' 'seq_pep/${species}.pep.fasta.pin' &&
            ln -s '${blast_path}.psq' 'seq_pep/${species}.pep.fasta.psq' && ls -l seq_pep/ &&
        #end if

        ## create the orthologe database symlinks to comply with how KOBAS wants them
        #if $ortholog.only == 'YES' and str($ortholog.species) != str($species):

            #if $ortholog.blast_opts_ortholog.choice == 'local':
                #set $blast_path = $ortholog.blast_opts_ortholog.localdb.fields.path
            #else if $ortholog.blast_opts_ortholog.choice == 'fasta':
                makeblastdb
                    -in '$ortholog.blast_opts_ortholog.fastadb'
                    -dbtype 'prot'
                    -out 'seq_pep/${ortholog.species}.pep.fasta' &&
            #else:
                #set $blast_path = $os.path.join($ortholog.blast_opts_ortholog.histdb.extra_files_path,'blastdb')
            #end if

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

            #if $blast_opts.choice != 'fasta':
                ln -s '${blast_path}.phr' 'seq_pep/${ortholog.species}.pep.fasta.phr' &&
                ln -s '${blast_path}.pin' 'seq_pep/${ortholog.species}.pep.fasta.pin' &&
                ln -s '${blast_path}.psq' 'seq_pep/${ortholog.species}.pep.fasta.psq' &&
            #end if
        #end if

        kobas-annotate
            -i '$infile'
            -t '$intype'
            -s '$species'
            -e '$evalue'
            -r $rank
            -c $coverage
            #if $ortholog.only == 'YES':
                -z '$ortholog.species'
            #end if
            -y seq_pep
            -q sqlite
            -p blastp
            -x blastx
            -o '$output'

        ]]>
    </command>
    <inputs>
        <param format="fasta" type="data" label="Input file" help="Input data file matching the input type." argument="--infile"/>
        <param type="select" label="Input type" argument="--intype" help="Input data type, default fasta:pro">
            <option value="fasta:pro">FASTA protein sequence</option>
            <option value="fasta:nuc">FASTA nucleotide sequence</option>
            <option value="blastout:xml">XML BLAST output</option>
            <option value="blastout:tab">Tabular BLAST output</option>
            <option value="id:uniprot">UniProtKB AC</option>
            <option value="id:ensembl">Ensembl Gene ID</option>
            <option value="id:ncbigene">Entrez Gene ID</option>
            <option value="id:refseqpro">Refseq Protein ID</option>
        </param>

        <conditional name="blast_opts">
            <expand macro="blastdb_selector"/>
        </conditional>

        <expand macro="input_kobasdb"/>

        <param format="sqlite" name="organismdb" type="data" label="Organism database" help="KOBAS organism database, available at http://kobas.cbi.pku.edu.cn/download.php"/>
        <param type="text" argument="--evalue" value="1e-5" label="E-value" help="Expect threshold for BLAST, default 1e-5"/>
        <param type="integer" argument="--rank" value="5" min="0" label="Rank cutoff" help="Rank cutoff for valid hits from BLAST result, default 5"/>
        <param type="integer" argument="--coverage" value="0" min="0" label="Subject coverage cutoff" help="subject coverage cutoff for BLAST, default 0"/>
        <conditional name="ortholog">
            <param name="only" type="select" argument="--ortholog" label="Only use orthologs" help="Whether only use orthologs for cross-species annotation or not, default NO (if only use orthologs, please provide the species abbreviation of your input)">
                <option value="NO">No</option>
                <option value="YES">Yes</option>
            </param>
            <when value="YES">
                <expand macro="input_kobasdb"/>
                <conditional name="blast_opts_ortholog">
                    <expand macro="blastdb_selector"/>
                </conditional>
            </when>
            <when value="NO"></when>
        </conditional>
    </inputs>
    <outputs>
        <data format="tabular" name="output"/>
    </outputs>

    <tests>
        <test>
            <param name="infile" value="kobas_annotate_input.fasta"/>
            <param name="intype" value="fasta:pro"/>
            <conditional name="blast_opts">
                <param name="choice" value="fasta"/>
                <param name="fastadb" value="aaa.pep.fasta" />
            </conditional>
            <param name="species" value="aaa"/>
            <param name="kobasdb" value="aaa.db"/>
            <param name="organismdb" value="organism.db"/>
            <output name="out_file1" file="kobas_annotate_output.txt"/>
        </test>
    </tests>

    <help>
@HELP_KOBAS_INFO@

**KOBAS Annotate**

Annotates an input set of genes with putative pathways and disease relationships based on mapping to genes with known annotations. It allows for both ID mapping and cross-species sequence similarity mapping.

@HELP_KOBAS_URL@
    </help>

    <expand macro="kobas_citations"/>

</tool>