<tool id="trinity_contig_exn50_statistic" name="Compute contig Ex90N50 statistic and Ex90 transcript count" version="@WRAPPER_VERSION@.0">
    <description>from a Trinity assembly</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
    </expand>
    <expand macro="stdio"/>
    <command><![CDATA[

    contig_ExN50_statistic.pl
        '$matrix'
        '$transcripts'
        > '$output'

    ]]></command>
    <inputs>
        <param format="tabular" name="matrix" type="data" label="Expression matrix" help="Matrix of normalized expression values produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool"/>
        <param format="fasta" name="transcripts" type="data" label="Transcripts" help="De novo assembly of RNA-Seq data"/>
    </inputs>
    <outputs>
        <data format="tabular" name="output" label="${tool.name} on ${on_string}: ExN50 statistics"/>
    </outputs>
    <tests>
        <test>
            <param name="matrix" value="count/contig_exn50_statistic/matrix.TMM.EXPR.matrix"/>
            <param name="transcripts" value="count/contig_exn50_statistic/Trinity.fasta"/>
            <output name="output" file="count/contig_exn50_statistic/ExN50.stats"/>
        </test>
    </tests>
    <help>
<![CDATA[
Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
This tool computes the N50 statistic limited to the top most highly expressed transcripts that represent x% of the total normalized expression data. This requires that you have first performed transcript abundance estimation with 'Align reads and estimate abundance for a de novo assembly of RNA-Seq data by Trinity' tool and that you have built the expression matrix with 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool. 

**Inputs**

It takes as input a transcriptome assembled with Trinity and the matrix of normalized expression values produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.

.. _Trinity: http://trinityrnaseq.github.io
]]>
    </help>
    <expand macro="citation" />
</tool>