<tool id="rseqc_insertion_profile" name="Insertion Profile" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>
     calculates the distribution of inserted nucleotides across reads
    </description>
    <macros>
        <import>rseqc_macros.xml</import>
    </macros>
    <expand macro="bio_tools"/>
    <expand macro="requirements"/>
    <expand macro="stdio"/>
    <version_command><![CDATA[insertion_profile.py --version]]></version_command>
    <command><![CDATA[
        @BAM_SAM_INPUTS@
        insertion_profile.py -i 'input.${extension}' -o output -q ${mapq} -s "${layout}"
        ]]>
    </command>
    <inputs>
        <expand macro="bam_sam_param"/>
        <expand macro="mapq_param"/>
        <expand macro="layout_param"/>
        <expand macro="rscript_output_param"/>
    </inputs>
    <outputs>
        <expand macro="pdf_output_data" filename="output.insertion_profile.pdf"/>
        <expand macro="xls_output_data" filename="output.insertion_profile.xls"/>
        <expand macro="rscript_output_data" filename="output.insertion_profile.r"/>
    </outputs>
    <tests>
        <test expect_num_outputs="3">
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
            <param name="rscript_output" value="true"/>
            <output name="outputpdf" file="output.insertion_profile.pdf" compare="sim_size"/>
            <output name="outputxls" file="output.insertion_profile.xls" ftype="tabular"/>
            <output name="outputr" file="output.insertion_profile_r"/>
        </test>
    </tests>
    <help><![CDATA[
insertion_profile.py
++++++++++++++++++++

Calculate the distributions of inserted nucleotides across reads. Note that to
use this funciton, CIGAR strings within SAM/BAM file should have ‘I’ operation.

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
++++++++++++++

Read-1 insertion profile:

.. image:: $PATH_TO_IMAGES/out.insertion_profile.R1.png
   :height: 600 px
   :width: 600 px
   :scale: 80 %

Read-2 insertion profile:

.. image:: $PATH_TO_IMAGES/out.insertion_profile.R2.png
  :height: 600 px
  :width: 600 px
  :scale: 80 %

@ABOUT@

]]>
    </help>
    <expand macro="citations"/>
</tool>