annotate data_manager/install_primer_scheme_bedfiles.xml @ 5:be70da9dc013 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_primer_scheme_bedfiles commit 68adfad76cdb5ff13ec9fb49895a3cde2c502514"

<tool id="data_manager_primer_scheme_bedfiles" name="BED-format primer scheme data manager" version="0.0.12" tool_type="manage_data" profile="19.05">
    <requirements>
        <requirement type="package" version="2.24.0">requests</requirement>
    </requirements>
    <!-- fetch all the primers in one go -->
    <command detect_errors="exit_code"><![CDATA[
    python '$__tool_directory__/install_primer_scheme_bedfiles.py'
        '${output_file}'
        #if $input.input_type == "ARTIC"
            --artic_primers '${input.primers}'
        #else 
            --primer_file '${input.primer_input}'
            --primer_name '${input.primer_name}'
            --primer_description '${input.primer_description}'
        #end if
    ]]></command>
    <inputs>
        <conditional name="input">
            <param name="input_type" label="Choose the source for primer schemes" type="select">
                <option value="ARTIC" selected="true">ARTIC SARS-CoV-2 Github page</option>
                <option value="history">History</option>
            </param>
            <when value="ARTIC">                    
                <param name="primers" type="select" multiple="true" label="SARS-CoV-2 Primers to fetch">
                    <option value="SARS-CoV-2-ARTICv1" selected="true">SARS-CoV-2 ARTIC v1</option>
                    <option value="SARS-CoV-2-ARTICv2" selected="true">SARS-CoV-2 ARTIC v2</option>
                    <option value="SARS-CoV-2-ARTICv3" selected="true">SARS-CoV-2 ARTIC v3</option>
                </param>
            </when>
            <when value="history">
                <param name="primer_input" label="Select history item" type="data" format="bed" />
                <param name="primer_name" label="Name for this primer scheme" type="text" 
                       help="Non-word characters will be removed from primer scheme name and spaces replaced with underscore (_)" />
                <param name="primer_description" label="Description for primer scheme" type="text" />
            </when>
        </conditional>
    </inputs>
    <outputs>
        <data name="output_file" format="data_manager_json"/>
    </outputs>
    <tests>
        <test>
            <param name="input_type" value="ARTIC" />
            <param name="primers" value="SARS-CoV-2-ARTICv1,SARS-CoV-2-ARTICv2,SARS-CoV-2-ARTICv3"/>
            <output name="output_file">
                <assert_contents>
                    <has_text text="ARTIC"/>
                </assert_contents>
            </output>        
        </test>
        <test>
            <param name="input_type" value="history" />
            <param name="primer_input" ftype="bed" value="sample1.bed" />
            <param name="primer_name" value="sample_primer" />
            <param name="primer_description" value="sample primer scheme" />
            <output name="output_file">
                <assert_contents>
                    <has_text text="sample_primer"/>
                </assert_contents>
            </output>        
        </test>
    </tests>
    <help><![CDATA[
        Amplicon sequencing for viral pathogens using the ARTIC_ pipeline or `PrimalSeq and iVar`_ relies on
        identifying primer locations in a reference sequence using BED format files. This 
        data manager populates a Galaxy tool data table, either from files provided via
        a history or via the ARTIC_ network Github repository.

        .. _PrimalSeq and iVar: https://genomebiology.biomedcentral.com/articles/10.1186/s13059-018-1618-7
        .. _ARTIC: https://artic.network/
    ]]></help>
    <citations>
      <citation type="doi">10.1186/s13059-018-1618-7</citation>
    </citations>
</tool>