annotate macros.xml @ 8:1c785a6b4d90 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/nextclade commit 017e25729a8ffd3722e87dfdf10ff4fd99c0babd"

<macros>
    <!-- same version number is used for nextclade and nextalign releases, even though they are distinct tools -->
    <token name="@TOOL_VERSION@">1.7.0</token>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@online{nextclade,
                title={nextclade},
                year = 2021,
                url = {https://github.com/nextstrain/nextclade},
                urldate = {2021-03-26}
                }
            </citation>
            <yield />
        </citations>
    </xml>

    <!--
        command
    -->
    <token name="@REF_FASTA@"><![CDATA[
    #if $reference_source.reference_source_selector == 'history':
        ln -f -s '$reference_source.ref_file' reference.fa &&
    #else:
        ln -f -s '$reference_source.ref_file.fields.path' reference.fa &&
    #end if
]]></token>

    <!--
        inputs
    -->

    <xml name="reference">
        <conditional name="reference_source">
            <param name="reference_source_selector" type="select" label="Choose the source for the reference genome">
                <option value="cached">Use a built-in genome</option>
                <option value="history">Use a genome from history</option>
            </param>
            <when value="cached">
                <param name="ref_file" type="select" label="Using reference genome" help="Select genome from the list">
                    <options from_data_table="all_fasta">
                        <filter type="sort_by" column="2"/>
                    </options>
                    <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file"/>
                </param>
            </when>
            <when value="history">
                <param name="ref_file" type="data" format="fasta" label="Use the following dataset as the reference sequence" help="You can upload a FASTA sequence to the history and use it as reference"/>
            </when>
        </conditional>
    </xml>

    <!--
        help
    -->
    <token name="@NEXTCLADE@"><![CDATA[
Nextclade is a tool that identifies differences between your sequences and a reference sequence, uses these differences to assign your sequences to clades, and reports potential sequence quality issues in your data.
You can use the tool to analyze sequences before you upload them to a database, or if you want to assign Nextstrain clades to a set of sequences.
]]></token>

</macros>