<tool id="trinity_stats" name="Trinity Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@">
    <description></description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements" />
    <command detect_errors="aggressive"><![CDATA[
    #if $input.ext.endswith(".gz")
        gunzip -c '$input' > input &&
    #else
        ln -s '$input' input &&
    #end if
    TrinityStats.pl input  > '$statsfile'
    ]]>
    </command>

    <inputs>
        <param name='input'  type="data" format="fasta,fasta.gz" label='Trinity Assembly' help='Trinity Assembled fasta file'/>
    </inputs>

    <outputs>
        <data name='statsfile' format='txt'/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="count/contig_exn50_statistic/Trinity.fasta"/>
            <output name="statsfile" file="count/trinityStats/statsfile.txt"/>
        </test>
        <test>
            <param name="input" value="count/contig_exn50_statistic/Trinity.fasta.gz"/>
            <output name="statsfile" file="count/trinityStats/statsfile.txt"/>
        </test>
    </tests>
    <help>
<![CDATA[
Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
This tool computes basic statistics of the assembly (such as stats for genes, transcripts, reconstruction size and N metrics).

**Inputs**

It takes as input a transcriptome assembled with Trinity.

.. _Trinity: https://github.com/trinityrnaseq/trinityrnaseq/wiki
]]>
    </help>
    <expand macro="citation" />
    <creator>
        <person givenName="Paul" familyName="Zierep" email="zierep@informatik.uni-freiburg.de" />
    </creator>
</tool>