annotate gene_to_trans_map.xml @ 17:7e3849997c91 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit c468d2b9613f88cc5f96f77ab1e0592d3c9ce707"

<tool id="trinity_gene_to_trans_map" name="Generate gene to transcript map" version="@WRAPPER_VERSION@">
    <description>for Trinity assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <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.
        The same file is automatically generated when running Trinity, this tool is only intended to be used when you don't (or no longer) have access to the one produced by Trinity.

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

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