<tool id="rseqc_clipping_profile" name="Clipping Profile" version="2.4galaxy1">
    <description>
     estimates clipping profile of RNA-seq reads from BAM or SAM file
    </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[clipping_profile.py --version]]></version_command>

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

    <inputs>
        <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
    </inputs>

    <outputs>
        <data format="pdf" name="outputpdf" from_work_dir="output.clipping_profile.pdf" />
        <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
        <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" />
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <output name="outputpdf" file="output.clipping_profile.pdf"/>
            <output name="outputxls" file="output.clipping_profile.xls"/>
            <output name="outputr" file="output.clipping_profile.r"/>
        </test>
    </tests>

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

This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
(This means your reads aligner should support clipped mapping).

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

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


Sample Output
++++++++++++++

.. image:: http://rseqc.sourceforge.net/_images/clipping_good.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>