<tool id="riassigner" name="RIAssigner" version="@TOOL_VERSION@+galaxy5" profile="21.09">
    <description>compute retention indices</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="creator"/>

    <xrefs>
        <xref type="bio.tools">riassigner</xref>
    </xrefs>

    <requirements>
        <requirement type="package" version="@TOOL_VERSION@">riassigner</requirement>
    </requirements>

    <command detect_errors="exit_code"><![CDATA[
        python -m RIAssigner --reference "$reference_section.reference" "$reference_section.reference.ext" "$reference_section.reference_rt_units" --query "$query_section.query" "$query_section.query.ext" "$query_section.query_rt_units" --method "$method" --output "output.${output.ext}" &&
        cp -r 'output.${output.ext}' '${output}'
        ]]>
    </command>

    <inputs>
        <section name="query_section" title="Query dataset" expanded="true">
            <param name="query" type="data" format="csv,tsv,msp">
                <label>Query compound list</label>
                <help><![CDATA[
            A list of compounds with retention times for which to compute the retention index.
            Expected columns for RT (oneof): ['rt', 'retention_time'].
            ]]></help>
            </param>
            <param name="query_rt_units" type="select" display="radio" help="Retention time units in the query file.">
                <option value="seconds" selected="true">Seconds</option>
                <option value="min">Minutes</option>
            </param>
        </section>
        <section name="reference_section" title="Reference dataset" expanded="true">
            <param name="reference" type="data" format="csv,tsv,msp">
                <label>Reference compound list</label>
                <help><![CDATA[
                A list of retention time and retention index pairs.
                Expected columns for RT (oneof): ['rt', 'retention_time'].
                Expected columns for RI (oneof): ['carbon_number', 'ri', 'retention_index'].
                ]]></help>
            </param>
            <param name="reference_rt_units" type="select" display="radio"
                   help="Retention time units in the reference file.">
                <option value="seconds" selected="true">Seconds</option>
                <option value="min">Minutes</option>
            </param>
        </section>
        <param label="Computation method" name="method" type="select" display="radio" help="Computation method to use.">
            <option value="kovats" selected="true">Kovats</option>
            <option value="cubicspline">CubicSpline</option>
        </param>
    </inputs>

    <outputs>
        <data label="RI using $method of ${query_section.query.element_identifier}" name="output" format="tsv"
              metadata_source="query">
            <change_format>
                <when input="query_section.query.ext" value="msp" format="msp" />
            </change_format>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="query" value="aplcms_aligned_peaks.csv" ftype="csv"/>
            <param name="query_rt_units" value="seconds"/>
            <param name="reference" value="Alkanes_20210325.csv" ftype="csv"/>
            <param name="reference_rt_units" value="seconds"/>
            <param name="method" value="kovats"/>
            <output name="output" file="results.tsv" ftype="tsv"/>
        </test>
    </tests>

    <help>
        <![CDATA[
        @HELP@
        ]]>
    </help>
    
    <citations>
        <citation type="doi">10.21105/joss.04337</citation>
    </citations>
</tool>