<tool id="rseqc_clipping_profile" name="Clipping Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>
     estimates clipping profile of RNA-seq reads from BAM or SAM file
    </description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>

    <expand macro="bio_tools"/>

    <expand macro="requirements" />

    <expand macro="stdio" />

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

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        clipping_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}"
        ]]>
    </command>

    <inputs>
        <expand macro="bam_param" />
        <expand macro="mapq_param" />
        <expand macro="layout_param" />
        <expand macro="rscript_output_param" />
    </inputs>

    <outputs>
        <expand macro="pdf_output_data" filename="output.clipping_profile.pdf" label="${tool.name} on ${on_string}: PDF"/>
        <expand macro="xls_output_data" filename="output.clipping_profile.xls" label="${tool.name} on ${on_string}: XML"/>
        <expand macro="rscript_output_data" filename="output.clipping_profile.r" label="${tool.name} on ${on_string}: Rscript"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
            <output name="outputxls" file="output.clipping_profile.xls" />
        </test>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <param name="rscript_output" value="true" />
            <output name="outputpdf" file="output.clipping_profile.pdf" compare="sim_size" />
            <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.

Minimum mapping quality
    Minimum mapping quality for an alignment to be considered as "uniquely
    mapped". default=30

Sequencing layout
    Denotes whether the sequecing was single-end (SE) or paired-end (PE).

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

.. image:: $PATH_TO_IMAGES/clipping_good.png
   :height: 600 px
   :width: 600 px
   :scale: 80 %

@ABOUT@

]]>
    </help>

    <expand macro="citations" />

</tool>