<tool id="trinity_samples_qccheck" name="RNASeq samples quality check" version="@WRAPPER_VERSION@">
    <description>for transcript quantification</description>
    <macros>
        <import>macros.xml</import>
    </macros>
    <expand macro="requirements">
        <requirement type="package" version="2.38.0">bioconductor-biobase</requirement>
        <requirement type="package" version="2.10.0">bioconductor-qvalue</requirement>
        <requirement type="package" version="2.0.6">r-cluster</requirement>
        <requirement type="package" version="1.1.24">r-fastcluster</requirement>
    </expand>
    <command detect_errors="aggressive"><![CDATA[

        ln -f -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" argument="--matrix" type="data" label="Expression matrix" help="output of abundance_estimates_to_matrix tool"/>
        <param format="tabular" name="samples" argument="--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.CPM.log2.prcomp.principal_components.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.CPM.log2.prcomp.principal_components.pdf"/>
                <element name="input.matrix.CPM.log2.sample_cor_matrix.pdf" compare="sim_size" delta="100" file="count/qcheck/input.matrix.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
=========== ================

This file can be generated with the 'Describe samples and replicates' tool.
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>

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