<tool id="samples_qccheck" name="RNASeq samples quality check" version="2.1.1">
    <description>for transcript quantification</description>
    <requirements>
        <requirement type="package" version="2.1.1">trinity</requirement>
        <requirement type="package" version="2.30.0">bioconductor-biobase</requirement>
        <requirement type="package" version="2.2.2">bioconductor-qvalue</requirement>
    </requirements>
    <stdio>
        <exit_code range="1:"/>
    </stdio>
    <command><![CDATA[

        ln -s "${matrix}" "input.matrix"

        &&

        PtR
        --matrix "input.matrix"

        --samples "${samples}"

        --CPM --log2 --compare_replicates

        &&

        PtR
        --matrix "input.matrix"

        --samples "${samples}"

        --CPM --log2 --sample_cor_matrix

        &&

        PtR
        --matrix "input.matrix"

        --samples "${samples}"

        --CPM --log2 --prin_comp 3

        && mkdir out_pdf
        && mv *rep_compare.pdf out_pdf/
        && mv *sample_cor_matrix.pdf out_pdf/
        && mv *principal_components.pdf out_pdf/

    ]]></command>
    <inputs>
        <param format="tabular" name="matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
        <param format="tabular" name="samples" type="data" label="Samples description" help="file describing samples and replicates"/>
    </inputs>
    <outputs>
        <collection name="reports" type="list" label="Quality check result files on ${on_string}">
            <discover_datasets pattern="__name__" ext="pdf" directory="out_pdf" />
        </collection>
    </outputs>
    <tests>
        <test>
            <param name="matrix" value="count/qcheck/matrix.counts.matrix"/>
            <param name="samples" value="count/samples.txt"/>
            <output_collection name="reports">
                <element name="wt_37.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_37.rep_compare.pdf"/>
                <element name="wt_GSNO.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_GSNO.rep_compare.pdf"/>
                <element name="wt_ph8.rep_compare.pdf" compare="sim_size" delta="100" file="count/qcheck/wt_ph8.rep_compare.pdf"/>
                <element name="input.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.principal_components.pdf"/>
                <element name="input.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/matrix.counts.matrix.minCol10.minRow10.CPM.log2.sample_cor_matrix.pdf"/>
            </output_collection>
        </test>
    </tests>
    <help>
<![CDATA[
Trinity_ assembles transcript sequences from Illumina RNA-Seq data.
This tool performs some Quality Checks on a RNASeq experiment, analysing the abundance estimation for different samples using a transcriptome assembled with Trinity.

**Inputs**

This tool uses the matrix produced by 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity' tool.

You must describe your samples and replicates with a tabular file looking like this:

=========== ================
ConditionA  CondA_replicate1
----------- ----------------
ConditionA  CondA_replicate2
----------- ----------------
ConditionB  CondB_replicate1
----------- ----------------
ConditionB  CondB_replicate2
----------- ----------------
ConditionC  CondC_replicate1
----------- ----------------
ConditionC  CondC_replicate2
----------- ----------------
ConditionC  CondC_replicate3
=========== ================

The names in column 2 must match the names given in the tool 'Build expression matrix for a de novo assembly of RNA-Seq data by Trinity'.

**Output**

This tool will produce several PDF files, see the following page for more information:

.. _Trinity manual: https://github.com/trinityrnaseq/trinityrnaseq/wiki/QC-Samples-and-Replicates


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

     <citations>
        <citation type="doi">10.1038/nbt.1883</citation>
    </citations>
</tool>