<tool id="samtools_idxstats" name="BAM mapping statistics" version="0.0.1">
    <description>samtools idxstats</description>
    <requirements>
        <requirement type="binary">samtools</requirement>
        <requirement type="package" version="0.1.19">samtools</requirement>
    </requirements>
    <version_command interpreter="python">samtools_idxstats.py --version</version_command>
    <command interpreter="python">samtools_idxstats.py "$input_bam" "${input_bam.metadata.bam_index}" "$out_tabular"</command>
    <inputs>
        <param name="input_bam" type="data" format="bam" label="Input BAM file" />
    </inputs>
    <outputs>
        <data name="out_tabular" format="tabular" label="$input_bam.name (idxstats)" />
    </outputs>
    <stdio>
        <!-- Assume anything other than zero is an error -->
        <exit_code range="1:" />
        <exit_code range=":-1" />
    </stdio>
    <tests>
        <test>
            <param name="input_bam" value="ex1.bam" ftype="bam" />
            <output name="out_tabular" file="ex1.idxstats.tabular" ftype="tabular" />
        </test>
    </tests>
    <help>
**What it does**

This tool runs the ``samtools idxstats`` command in the SAMtools toolkit.

Input is a sorted and indexed BAM file, the output is tabular with
four columns (one row per reference sequence plus a final line for
unmapped reads):

====== =================================================================================
Column Description
------ ---------------------------------------------------------------------------------
     1 Reference sequence identifier
     2 Reference sequence length
     3 Number of mapped reads
     4 Number of placed but unmapped reads (typically unmapped partners of mapped reads)
====== =================================================================================

Example output from a *de novo* assembly:

========== ====== ====== =====
contig_1   170035  98397     0
contig_2   403835 199564     0
contig_3   553102 288189     0
...           ...    ...   ...
contig_603    653     50     0
contig_604    214      6     0
\*              0      0 50320
========== ====== ====== =====

In this example there were 604 contigs, each with one line in the output table,
plus the final row (labelled with an asterisk) representing 50320 unmapped reads.
In this BAM file, the final column was otherwise zero.


**Citation**

If you use this Galaxy tool in work leading to a scientific publication please
cite:

Heng Li et al (2009). The Sequence Alignment/Map format and SAMtools.
Bioinformatics 25(16), 2078-9.
http://dx.doi.org/10.1093/bioinformatics/btp352

Peter J.A. Cock (2013), Galaxy wrapper for the samtools idxstats command
http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats

This wrapper is available to install into other Galaxy Instances via the Galaxy
Tool Shed at http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats
    </help>
</tool>