<macros>
    <token name="@TOOL_VERSION@">1.5</token>
    <xml name="requirements">
        <requirements>
            <requirement type="package" version="@TOOL_VERSION@">flair</requirement>
            <yield />
        </requirements>
    </xml>

    <xml name="version_command">
        <version_command>flair.py --version</version_command>
    </xml>

    <token name="@PREPARE_REF@"><![CDATA[
        #if str($reference_source_genome.ref_selector_genome) == 'history':
            #set reference = $reference_source_genome.reffile
            #set ext = $reference.ext
            samtools faidx 'reference.fa' 2>&1 || echo "Error running samtools faidx for indexing fasta reference for flair" >&2 &&
        #else
            #set reference = $reference_source_genome.reffile.fields.path
            #set ext = $reference_source_genome.reffile.fields.path
        #end if
        #if $ext.endswith(".gz"):
            gunzip -c '$reference' > reference.fa &&
        #else:
            ln -sf '$reference' reference.fa &&
        #end if
    ]]></token>

    <xml name="reference_interface">
        <conditional name="reference_source_genome">
            <param name="ref_selector_genome" type="select" label="Choose the source for the reference genome">
                <option value="cached">Locally cached</option>
                <option value="history">History</option>
            </param>
            <when value="cached">
                <param name="reffile" argument="-g" type="select" label="Reference genome">
                        <options from_data_table="fasta_indexes">
                            <validator type="no_options" message="A built-in reference genome is not available for the build associated with the selected input file" />
                        </options>
                </param>
            </when>
            <when value="history">
                <param name="reffile" argument="-g" type="data" format="fasta,fasta.gz" label="Reference" help="Reference sequence" />
            </when>
        </conditional>
    </xml>

    <token name="@description@">

**FLAIR** FLAIR (Full-Length Alternative Isoform analysis of RNA) for the correction, isoform definition, and alternative splicing analysis of noisy reads. FLAIR has primarily been used for nanopore cDNA, native RNA, and PacBio sequencing reads.
FLAIR can be run optionally with short-read data to help increase splice site accuracy of the long read splice junctions. FLAIR uses multiple alignment steps and splice site filters to increase confidence in the set of isoforms defined from noisy data. FLAIR was designed to be able to sense subtle splicing changes in nanopore data from Tang et al. (2018).
It is recommended to combine all samples together prior to running flair-collapse for isoform assembly by concatenating corrected read psl or bed files together. Following the creation of an isoform reference from flair-collapse, consequent steps will assign reads from each sample individually to isoforms of the combined assembly for downstream analyses.

    </token>

    <token name="@citation@">

Author: Florian Heyl

    </token>
    <xml name="citations">
        <citations>
            <citation type="doi">10.1038/s41467-020-15171-6</citation>
        </citations>
    </xml>
</macros>