<tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@GALAXY_VERSION@">
    <description>
        reads mapping statistics for a provided 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[bam_stat.py --version]]></version_command>

    <command><![CDATA[
        @BAM_SAM_INPUTS@
        bam_stat.py -i 'input.${extension}' -q ${mapq} > '${output}'
        ]]>
    </command>

    <inputs>
        <expand macro="bam_sam_param" />
        <expand macro="mapq_param" />
    </inputs>

    <outputs>
        <data format="txt" name="output" label="${tool.name} on ${on_string}: stats"/>
    </outputs>

    <tests>
        <test>
            <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam" />
            <output name="output" file="output.bamstats.txt" />
        </test>
    </tests>

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

This program is used to calculate reads mapping statistics from provided BAM
file.  This script determines "uniquely mapped reads" from `mapping quality
<http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores>`_,
which quality the probability that a read is misplaced (Do NOT confused with
sequence quality, sequence quality measures the probability that a base-calling
was wrong) .

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

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

Minimum mapping quality
    Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)

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

- Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
- Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
- Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
- Uniquely mapped Reads = {Splice reads} + {Non-splice reads}

@ABOUT@

]]>
    </help>

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