annotate gene_to_trans_map.xml @ 0:83c862e77b99 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit e23a8ad798830209db722d5496d19ec7a5e06214

<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"/>
    <expand macro="stdio"/>
    <command><![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>