<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.0.11</token>
    <token name="@VERSION_SUFFIX@">0</token>    
    <token name="@PROFILE@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">jasminesv</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command>jasmine</version_command>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@online{jasmine,
              author = {Melanie Kirsche},
              title = {jasmine},
              year = 2021,
              url = {https://github.com/mkirsche/Jasmine},
              urldate = {2021-01-13}
            }</citation>
        </citations>
    </xml>
    <!--
        Command
    -->
    <token name="@REF_FASTA@"><![CDATA[
        #if $dup_to_ins.reference_source.reference_source_selector == 'history':
            ln -f -s '$dup_to_ins.reference_source.ref_file' reference.fa &&
        #else:
            ln -f -s '$dup_to_ins.reference_source.ref_file.fields.path' reference.fa &&
        #end if
    ]]></token>

    <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"/>
                        <validator type="no_options" message="No reference genomes are available"/>
                    </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,fastq" label="Use the following dataset as the reference sequence" help="You can upload a FASTA or FASTQ sequence to the history and use it as reference"/>
            </when>
        </conditional>
    </xml>
    <!--
        Help
    -->

    <token name="@WID@"><![CDATA[
*Jasmine*, or Jointly Accurate Sv Merging with Intersample Network Edges is a tool used to merge structural variants (SVs) across samples. Each sample has a number of SV calls, consisting of position information (chromosome, start, end, length), type and strand information, and a number of other values. Jasmine represents the set of all SVs across samples as a network, and uses a modified minimum spanning forest algorithm to determine the best way of merging the variants such that each merged variants represents a set of analogous variants occurring in different samples.
]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information is available in the `github <https://github.com/mkirsche/Jasmine>`_.
    ]]></token>
</macros>