view virAnnot_rps2tsv.xml @ 0:bbaa89f070f4 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/virAnnot commit 3a3b40c15ae5e82334f016e88b1f3c5bbbb3b2cd

<tool id="virAnnot_rps2tsv" name="virAnnot Rps2tsv" version="1.0.0+galaxy0" profile="21.05">
    <description>Convert xml rpstblast results to tab file with taxonomic informations</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <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="10" />
                    <has_n_lines n="105" />
                </assert_contents>
            </output>
         </test>
         <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_text text="pfam01333, Apocytochr_F_C, Apocytochrome F" />
                </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
ds2020-267_120  339 pfam01333   gnl|CDD|366578  0.000848733 197 325 -3  pfam01333, Apocytochr_F_C, Apocytochrome F, C-terminal.  This is a sub-family of cytochrome C. See pfam00034.   Eukaryota(227);Bacteria(73);

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