<tool id="smap_selector" name="SMAP-selector" version="0.1.0" python_template_version="3.5">
    <requirements>
        <!--<requirement type="package">smap-design</requirement>-->
        <requirement type="package">biopython</requirement>
        <requirement type="package">gffutils</requirement>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        ln -s $fasta_file species_fasta.fa;
        ln -s $gff_file species.gff3;
        ln -s $gene_families_file families_file.txt;
        #if $interest_input_selector.interest_input == "genes":
            ln -s $interest_input_selector.genes_file genes_file.txt;
        #else
            ln -s $interest_input_selector.homology_groups_file hom_groups_file.txt;
        #end if
        python3 $__tool_directory__/Get_fasta_and_gff_for_selected_hom_groups_extended_flanking_region.py ./species.gff3 ./species_fasta.fa ./families_file.txt $species --region $region
        #if $interest_input_selector.interest_input == "genes":
            --genes genes_file.txt
        #else
            --hom_groups hom_groups_file.txt
        #end if
        ;
        rm species.gff3;  
    ]]></command>
    <inputs>
        <param name="species" type="text" label="Species, corresponding with species indicated in the gene family info file"/>
        <param name="gene_families_file" type="data" format="tsv,tabular" label="gene family information file (tab-delimited) for the (coding) genes, separated per gene family type"/>
        <param name="fasta_file" type="data" format="fasta" label="FASTA file containing the genomic sequence of the species"/>
        <param name="gff_file" type="data" format="gff,gff3" label="gff3 file (tab-delimited) of the species containing gene, CDS, and exon features with positions relative to the fasta file"/>
        <conditional name="interest_input_selector">
            <param name="interest_input" type="select">
                <option value="genes">list with genes of interest</option>
                <option value="homology_groups">list with homology groups of interest</option>
            </param>
            <when value="genes">
                <param name="genes_file" type="data" format="txt" label="Genes file"/>
            </when>
            <when value="homology_groups">
                <param name="homology_groups_file" type="data" format="txt" label="Homology groups file"/>
            </when>
        </conditional>
        <param argument="--region" type="integer" value="0" label="Region to extend the FASTA sequence of the genes of interest on both sides with the given number of basepairs or with the maximum possible" help="default: 0"/>
    </inputs>
    <outputs>
        <data format="fasta" name="fasta_outputs" label="SMAP-Selector FASTA outputs">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.fasta" ext="fasta" format="fasta" visible="true" assign_primary_output="true"/>
        </data>
        <data format="gff" name="gff_outputs" label="SMAP-Selector GFF outputs">
            <discover_datasets pattern="(?P&lt;designation&gt;.+)\.gff" ext="gff" visible="true" format="gff" assign_primary_output="true"/>
        </data>
    </outputs>
    <help><![CDATA[
        TODO: Fill in help.
    ]]></help>
</tool>