<tool id="virAnnot_rps2tsv" name="virAnnot Rps2tsv" version="@TOOL_VERSION@+galaxy0" profile="21.05">
    <description>Convert xml rpstblast results to tab file with taxonomic informations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="xrefs"/>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
        python '$__tool_directory__/rps2tsv.py'
            -x '$rps_xml'
            -e '$max_evalue'
            -o '$output'
    ]]></command>
    <inputs>
        <param type="data" name="rps_xml" format="xml" label="RPSTBlast results file" />
        <param type="select" name="max_evalue" label="Maximum evalue">
            <option value="0">0</option>
            <option value="0.1">0.1</option>
            <option value="0.01">0.01</option>
            <option value="0.001" selected="true">0.001</option>
            <option value="0.0001">0.0001</option>
        </param>
    </inputs>
    <outputs>
        <data name="output" format="tabular" from_work_dir="rps_result.tab" />
    </outputs>
    <tests>
        <test>
            <param name="rps_xml" value="rps_test.xml"/>
            <param name="max_evalue" value="0.0001"/>
            <output name="output" file="rps_test.tab">
                <assert_contents>
                    <has_n_columns n="11" />
                    <has_n_lines n="5" />
                    <has_text text="pfam00680, RdRP_1" />
                </assert_contents>
            </output>
         </test>
    </tests>
    <help><![CDATA[
        
This module takes as input rps XML file from rps motives annotation.
The standard maximum evalue is 0.0001 [default value].
The expected result is a tabular file. See example:
#query_id   query_length    cdd_id  hit_id  evalue  startQ  endQ    frame   description superkingdom    pident
ds2020-267_4    2297    pfam00680   gnl|CDD|279070  3.12197e-05 995 1873    -2  pfam00680, RdRP_1, RNA dependent RNA polymerase.    Viruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)    16.986
ds2020-267_5    2029    pfam00680   gnl|CDD|279070  8.86955e-06 840 1706    3   pfam00680, RdRP_1, RNA dependent RNA polymerase.    Viruses(1);Riboviria(1);Orthornavirae(1);Pisuviricota(1)    17.974
ds2020-267_6    1860    pfam02123   gnl|CDD|280316  1.27376e-17 1147    1764    -1  pfam02123, RdRP_4, Viral RNA-directed RNA-polymerase.  This family includes RNA-dependent RNA polymerase proteins (RdRPs) from Luteovirus, Totivirus and Rotavirus. Viruses(1);Riboviria(1);Orthornavirae(1);Resentoviricetes(1)    23.671


    ]]></help>
    <expand macro="citations" />
</tool>