<tool id="rseqc_read_duplication" name="Read Duplication" version="2.4galaxy1">
    <description>determines reads duplication rate with sequence-based and mapping-based strategies</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_duplication.py --version]]></version_command>

    <command><![CDATA[
        read_duplication.py -i $input -o output -u $upLimit
        ]]>
    </command>

    <inputs>
        <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
        <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
    </inputs>

    <outputs>
        <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/>
        <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/>
        <data format="txt" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" />
        <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <output name="outputxls" file="output.pos.DupRate.xls"/>
            <output name="outputseqxls" file="output.seq.DupRate.xls"/>
            <output name="outputr" file="output.DupRate_plot.r"/>
        </test>
    </tests>

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

Two strategies were used to determine reads duplication rate:

* Sequence based: reads with exactly the same sequence content are regarded as duplicated reads.
* Mapping based: reads mapped to the same genomic location are regarded as duplicated reads. For splice reads, reads mapped to the same starting position and splice the same way are regarded as duplicated reads.

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

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

Upper Limit of Plotted Duplicated Times (default=500)
    Only used for plotting.

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

1. output.dup.pos.DupRate.xls: Read duplication rate determined from mapping position of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
2. output.dup.seq.DupRate.xls: Read duplication rate determined from sequence of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
3. output.DupRate_plot.r: R script to generate pdf file
4. output.DupRate_plot.pdf: graphical output generated from R script

.. image:: http://rseqc.sourceforge.net/_images/duplicate.png
   :height: 600 px
   :width: 600 px
   :scale: 80 %

-----

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>