<tool id="edu.tamu.cpt2.phage.annotation_table" name="Annotation Table" version="20.0.0.1">
    <description>from gff3 formatted datasets</description>
    <macros>
        <import>macros.xml</import>
    
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.10.1">jinja2</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[
@GENOME_SELECTOR_PRE@

python '$__tool_directory__/phage_annotation_table.py'
'$gff3_data'
@GENOME_SELECTOR@
--types "$extraTypes"
--reportTemplateName "$report_format"
--annotationTableCols "$cols,$gaf_cols"
#if $gaf_data:
--gafData "$gaf_data"
#end if
'$checkSubfeats'
> '$output']]></command>
    <inputs>
        <expand macro="gff3_input"/>
        <expand macro="genome_selector"/>
        <param label="Extra sub-feature types to include (Comma-separated, Will always include gene)" optional="True" name="extraTypes" type="text" value=""/>
        <param label="Columns" type="select" name="cols" multiple="True">
            <option value="rid" selected="true">Record ID</option>
            <option value="id" selected="true">ID</option>
            <option value="type" selected="true">Type</option>
            <option value="name" selected="true">Name</option>
            <option value="location" selected="true">Location</option>
            <option value="start" selected="true">Feature Start</option>
            <option value="end" selected="true">Feature End</option>
            <option value="strand" selected="true">Strand</option>
            <option value="length" selected="true">Length</option>
            <option value="sd_seq" selected="true">SD sequence</option>
            <option value="sd_spacing" selected="true">SD spacing</option>
            <option value="start_codon" selected="true">Start codon</option>
            <option value="stop_codon" selected="true">Stop codon</option>
            <option value="ig_dist" selected="true">Distance to next upstream feature</option>
            <option value="upstream_feature__name" selected="true">Name of upstream feature</option>
            <option value="owner" selected="true">Owner</option>
            <option value="date_created" selected="true">Date created</option>
            <option value="date_last_modified" selected="true">Date last modified</option>
            <option value="notes" selected="true">Notes</option>
            <option value="description" selected="true">Description</option>
            <option value="product" selected="true">Product</option>
            <option value="dbxrefs" selected="true">DBxrefs</option>
            <option value="qualifiers" selected="true">Qualifiers</option>
        </param>
        <param label="GAF Data" name="gaf_data" type="data" format="tabular" optional="True" help="Optional GAF Data Table. This usually comes from the CPT CACAO GAF Data Export tool. The [GAF] Columns below are ONLY available when this data is populated."/>
        <param label="GAF Columns" type="select" name="gaf_cols" multiple="True">
            <!-- GAF Specific Fields -->
            <option value="gaf_annotation_extension" selected="false">GAF Annotation Extension</option>
            <option value="gaf_aspect" selected="false">GAF Aspect</option>
            <option value="gaf_assigned_by" selected="false">GAF Assigned By</option>
            <option value="gaf_date" selected="false">GAF Date</option>
            <option value="gaf_db" selected="false">GAF DB</option>
            <option value="gaf_db_reference" selected="false">GAF DB Reference</option>
            <option value="gaf_evidence_code" selected="false">GAF Evidence Code</option>
            <option value="gaf_gene" selected="false">GAF Gene</option>
            <option value="gaf_go_id" selected="false">GAF GO ID</option>
            <option value="gaf_go_term" selected="false">GAF GO Term</option>
            <option value="gaf_id" selected="false">GAF ID</option>
            <option value="gaf_notes" selected="false">GAF Notes</option>
            <option value="gaf_owner" selected="false">GAF Owner</option>
            <option value="gaf_with_or_from" selected="false">GAF with_or_from</option>
        </param>
        <param name="checkSubfeats" label="Search sub-features for fields if gene does not define them" type="boolean" truevalue="--searchSubs" falsevalue=""/>
        <param label="Report Format" type="select" name="report_format">
            <option value="phageqc_report_annotation_table.html" selected="true">HTML Table</option>
            <option value="phageqc_report_annotation_table.tsv">Tabular (Excel Compatible) Table</option>
        </param>
    </inputs>
    <outputs>
        <data format="html" name="output">
            <change_format>
                <when format="tabular" input="report_format" value="phageqc_report_annotation_table.tsv"/>
            </change_format>
        </data>
    </outputs>
    <tests>
        <test>
            <param name="reference_genome_source" value="history"/>
            <param name="genome_fasta" value="NC_001416_Table_In.fasta"/>
            <param name="gff3_data" value="NC_001416_Table_In.gff3"/>
            <param name="report_format" value="phageqc_report_annotation_table.html"/>
            <output name="output" file="PhageTable_Out.html"/>
        </test>
        <test>
            <param name="reference_genome_source" value="history"/>
            <param name="genome_fasta" value="NC_001416_Table_In.fasta"/>
            <param name="gff3_data" value="NC_001416_Table_In.gff3"/>
            <param name="report_format" value="phageqc_report_annotation_table.tsv"/>
            <output name="output" file="PhageTable_Out.tabular"/>
        </test>
    </tests>
    <help><![CDATA[
Generate an "annotation table" of a genome, with user-configurable data columns
]]></help>
    <expand macro="citations"/>
</tool>