<tool id="rseqc_read_quality" name="Read Quality" version="2.4galaxy1">
    <description>determines Phred quality score</description>

    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <requirements>
        <expand macro="requirement_package_r" />
        <expand macro="requirement_package_numpy" />
        <expand macro="requirement_package_rseqc" />
    </requirements>

    <expand macro="stdio" />

    <version_command><![CDATA[read_quality.py --version]]></version_command>

    <command><![CDATA[
        read_quality.py
            --input-file $input
            --out-prefix output
            -r $reduce
            --mapq $mapq
        ]]>
    </command>

    <inputs>
        <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
        <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
        <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
    </inputs>

    <outputs>
        <data format="txt" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" />
        <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" />
        <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" />
    </outputs>

    <!-- Unable to succefully run this script with test data
    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig"/>
            <output name="outputr" file="output.qual.r"/>
            <output name="outputheatpdf" file="output.qual.heatmap.pdf"/>
            <output name="outputboxpdf" file="output.qual.boxplot.pdf"/>
        </test>
    </tests>
    -->

    <help><![CDATA[
read_quality.py
+++++++++++++++

According to SAM specification, if Q is the character to represent "base calling quality"
in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
returns an integer representing the Unicode code point of the character when the argument
is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used
to measure "reliability" of base-calling, for example, phred quality score of 20 means
there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there
is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P,
here P is probability that base-calling is wrong.

Inputs
++++++++++++++

Input BAM/SAM file
    Alignment file in BAM/SAM format.

Ignore phred scores less than this number (default=1000)
    To avoid making huge vector in R, nucleotide with certain phred score represented less than this number will be ignored. Increase this number save more memory while reduce precision. This option only applies to the 'boxplot'.

Output
++++++++++++++

1. output.qual.r
2. output.qual.boxplot.pdf
    .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.plot.png
        :height: 600 px
        :width: 600 px
        :scale: 80 %
3. output.qual.heatmap.pdf
    .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.heatmap.png
        :height: 600 px
        :width: 600 px
        :scale: 80 %

Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")

-----

About RSeQC
+++++++++++

The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.

The RSeQC package is licensed under the GNU GPL v3 license.

.. image:: http://rseqc.sourceforge.net/_static/logo.png

.. _RSeQC: http://rseqc.sourceforge.net/
]]>
    </help>

    <expand macro="citations" />

</tool>