annotate gene_to_trans_map.xml @ 9:1b04880ff362 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/trinity commit 9dcdb5348f7439d0ce1e44ed23ad226beb4ae6d4

<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="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>