<?xml version="1.0"?>
<macros>
    <token name="@TOOL_VERSION@">1.0.4</token>
    <token name="@PROFILE@">20.01</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="1.9">samtools</requirement>
            <requirement type="package" version="@TOOL_VERSION@">irissv</requirement>
        </requirements>
    </xml>
    <xml name="version_command">
        <version_command>iris</version_command>
    </xml>
    <xml name="citations">
        <citations>
            <citation type="bibtex">@online{iris,
              author = {Melanie Kirsche},
              title = {iris},
              year = 2021,
              url = {https://github.com/mkirsche/Iris},
              urldate = {2021-01-13}
            }</citation>
        </citations>
    </xml>

    <!--
        command
    -->

    <token name="@REF_FASTA@"><![CDATA[
        #if $reference_source.reference_source_selector == 'history':
            #set reference = $reference_source.ref_file
            #set ext = $reference.ext
        #else:
            #set reference = $reference_source.ref_file.fields.path
            #set ext = $reference_source.ref_file.fields.path
        #end if
        #if $ext.endswith('.gz'):
            gunzip -c '$reference' > reference &&
        #else:
            ln -sf '$reference' reference &&
        #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,fasta.gz,fastq,fastq.gz" 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[
*irissv*, or Implement for Refining Insertion Sequences is a tool which corrects the sequences of structural variant calls (currently only insertions). It uses FalconSense to obtain consensus sequences of the reads surrounding each variant and aligns these sequences back to the reference at the insertion site, resulting in an insertion which takes into account the aggregate information of all supporting reads.
    ]]></token>
    <token name="@REFERENCES@"><![CDATA[
More information is available in the `github <https://github.com/mkirsche/Iris>`_.
    ]]></token>
</macros>