<tool id="pick_plasmids_containing_genes" name="Pick plasmids containing genes" version="0.1.0">
    <description>Pick plasmids containing specific genes</description>
    <requirements>
    </requirements>
    <command detect_errors="exit_code"><![CDATA[
        '$__tool_directory__/pick_plasmids_containing_genes.py'
        --plasmids
        #for $plasmid in $plasmids:
          '${plasmid}'
        #end for
        --concatenated_abricate_reports '${concatenated_abricate_reports}'
        --abricate_report_screening_file '${screening_file.fields.path}'
        --outdir outdir
    ]]></command>
    <inputs>
        <param name="plasmids" type="data_collection" collection_type="list" format="fasta" />
        <param name="concatenated_abricate_reports" type="data" format="tabular" />
        <param name="screening_file" type="select" format="tabular">
	    <options from_data_table="abricate_report_screening_files">
	        <validator type="no_options" message="No abricate report screening files are available" />
            </options>
	</param>
    </inputs>
    <outputs>
        <collection name="output" type="list" label="Output plasmids">
            <discover_datasets pattern="__name__" format="fasta" directory="outdir" />
        </collection>
    </outputs>
    <tests>
        <test>
	    <param name="plasmids">
                <collection type="list">
                    <element name="SRR9113487_plasmid_1068" value="SRR9113487_plasmid_1068.fasta" ftype="fasta" />
                    <element name="SRR9113487_plasmid_1550" value="SRR9113487_plasmid_1550.fasta" ftype="fasta" />
                    <element name="SRR9113487_plasmid_2719" value="SRR9113487_plasmid_2719.fasta" ftype="fasta" />
                    <element name="SRR9113487_plasmid_739" value="SRR9113487_plasmid_739.fasta" ftype="fasta" />
                    <element name="SRR9113487_plasmid_839" value="SRR9113487_plasmid_839.fasta" ftype="fasta" />
                    <element name="SRR9113487_plasmid_novel_0" value="SRR9113487_plasmid_novel_0.fasta" ftype="fasta" />
                </collection>
            </param>
            <param name="concatenated_abricate_reports" value="concatenated_abricate_reports.tsv" ftype="tabular"/>
            <param name="screening_file" value="screening_file_1"/>
            <output file="outdir/SRR9113487_plasmid_2719.fasta" ftype="fasta"/>
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>