<tool id="pick_plasmids_containing_genes" name="Pick plasmids containing genes" version="0.2.0">
    <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}'
        #if str( $screening_file_source.screening_file_source_selector ) == "tool_data_table":
          #set $input_screening_file = str( $screening_file_source.screening_file.fields.path )
        #else:
          #set $input_screening_file = str( $screening_file_source.screening_file )
        #end if
        --abricate_report_screening_file '${input_screening_file}'
        --outdir outdir &&
        cp '${input_screening_file}' '${output_screening_file}'
    ]]></command>
    <inputs>
        <conditional name="screening_file_source">
            <param name="screening_file_source_selector" type="select" label="Select a gene screening file from your history or use one from a tool data table?"
                   help="Screening files must be stored in the 'abricate_report_screening_files' tool data table">
                <option value="tool_data_table">From tool data table</option>
                <option value="history">From history</option>
            </param>
            <when value="tool_data_table">
                <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>
            </when>
            <when value="history">
                <param name="screening_file" type="data" format="tabular" label="Gene screening file" help="A two-column tab-delimited file with gene names and regular expressions" />
            </when>
        </conditional>
        <param name="plasmids" type="data_collection" collection_type="list" format="fasta" />
        <param name="concatenated_abricate_reports" type="data" format="tabular" />
    </inputs>
    <outputs>
        <collection name="output_plasmids" type="list" label="Output plasmids">
            <discover_datasets pattern="__name__" format="fasta" directory="outdir" />
        </collection>
        <data name="output_screening_file" format="tabular" />
    </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_source.screening_file_source_selector" value="tool_data_table" />
            <param name="screening_file_source.screening_file" value="screening_file_1"/>
            <output_collection name="output_plasmids" type="list" count="1" />
        </test>
        <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_source.screening_file_source_selector" value="history" />
            <param name="screening_file_source.screening_file" value="abricate_report_screening_file_1.tsv"/>
            <output_collection name="output_plasmids" type="list" count="1" />
        </test>
    </tests>
    <help><![CDATA[
    ]]></help>
    <citations>
    </citations>
</tool>