<tool id="trinity_super_transcripts" name="Generate SuperTranscripts" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="21.05">
    <description>from a Trinity assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
       Trinity_gene_splice_modeler.py --incl_malign --trinity_fasta '$assembly'
    ]]></command>
    <inputs>
        <param format="fasta" name="assembly" type="data" label="Trinity assembly"/>
    </inputs>
    <outputs>
        <data format="fasta" name="seqs" from_work_dir="trinity_genes.fasta" label="${tool.name} on ${on_string}: SuperTranscripts sequences"/>
        <data format="gtf" name="annotation" from_work_dir="trinity_genes.gtf" label="${tool.name} on ${on_string}: SuperTranscripts strcture annotation"/>
        <data format="clustal" name="malign" from_work_dir="trinity_genes.malign" label="${tool.name} on ${on_string}: multiple alignment of SuperTranscripts"/>
    </outputs>
    <tests>
        <test>
            <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
            <output name="seqs" file="supertranscripts/trinity_genes.fasta" sort="True" />
            <output name="annotation" file="supertranscripts/trinity_genes.gtf" sort="True" />
            <output name="malign" file="supertranscripts/trinity_genes.malign" />
        </test>
    </tests>
    <help>
        SuperTranscripts provide a gene-like view of the transcriptional complexity of a gene. SuperTranscripts were originally defined by Nadia Davidson, Anthony Hawkins, and Alicia Oshlack as described in their publication "SuperTranscripts: a data driven reference for analysis and visualisation of transcriptomes" Genome Biology, 2017. SuperTranscripts are useful in the context of genome-free de novo transcriptome assembly in that they provide a genome-like reference for studying aspects of the gene including differential transcript usage (aka. differential exon usage) and as a substrate for mapping reads and identifying allelic polymorphisms.

        A SuperTranscript is constructed by collapsing unique and common sequence regions among splicing isoforms into a single linear sequence.

        .. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
    </help>

    <expand macro="citation" />
</tool>