annotate gene_to_trans_map.xml @ 8:c2c039e421af draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 5098e1bf7037e204f24fa1cbf7c3749bf0779550

<tool id="trinity_gene_to_trans_map" name="Generate gene to transcript map" version="@WRAPPER_VERSION@.0">
    <description>for Trinity assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements"/>
    <command detect_errors="aggressive"><![CDATA[
       get_Trinity_gene_to_trans_map.pl "$assembly" > "$map"
    ]]></command>
    <inputs>
        <param format="fasta" name="assembly" type="data" label="Trinity assembly"/>
    </inputs>
    <outputs>
        <data format="tabular" name="map" label="${tool.name} on ${on_string}: Genes to transcripts map"/>
    </outputs>
    <tests>
        <test>
            <param name="assembly" value="raw/Trinity.fasta" ftype="fasta"/>
            <output name="map" file="raw/map.tsv" />
        </test>
    </tests>
    <help>
        Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
        This tool produces a file containing correspondance between gene ids and transcript ids based on the name of transcripts assembled by Trinity.
        The output file is intended to be used by the "Align reads and estimate abundance" tool.

        .. _Trinity: http://trinityrnaseq.github.io
    </help>

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