<tool id="sam_stats" name="sam-stats" version="1.38.763">
    <description> - Compute statistics from SAM or BAM files</description>

    <requirements>
        <requirement type="package" version="1.1.2-806">ea-utils</requirement>
    </requirements>

    <stdio>
        <exit_code range="1:" level="fatal" description="Unknown error occurred" />
    </stdio>

    <command><![CDATA[
        sam-stats
        $trackMultAlign
        $reportAllChr
        #if $rnaSeqStats:
        -R $rnaSeqStatsFile
        #end if
        #if $input.extension == "bam":
        -B
        #end if
        -S $histBinSize
        $input
        > $samStats
    ]]>
    </command>

    <inputs>
        <param format="sam, bam" name="input" type="data" label="SAM/BAM File" />
        <param name="trackMultAlign" type="boolean" value="False" truevalue="-D" falsevalue="" label="Keep track of multiple alignments (slower!)" />
        <param name="reportAllChr" type="boolean" value="False" truevalue="-A" falsevalue="" label="Report all chr sigs, even if there are more than 1000" />
        <!-- <param name="numReadsSubsample" type="integer" value="1000000" min="1" max="1000000" label="Number of reads to sample for per-base statistics (max 1,000,000)" /> -->
        <param name="histBinSize" type="integer" value="30" min="1" label="Number of bins per chromosome for reads by chromosome &quot;histogram&quot;" />
        <param name="rnaSeqStats" type="boolean" value="False" label="Output RNA-Seq statistics (coverage, 3 prime bias, etc.)" />
    </inputs>

    <outputs>
        <data format="tabular" name="samStats" label="${tool.name} on ${on_string}"/>
        <data format="tabular" name="rnaSeqStatsFile" label="${tool.name} on ${on_string} (RNA-Seq Stats)"> <filter>rnaSeqStats</filter>
        </data>
    </outputs>

    <tests>
        <test>
            <param name="input" value="test.sam" />
            <output name="samStats" file="testout.txt" />
        </test>
    </tests>

    <help><![CDATA[
Overview
--------
sam-stats computes varius statics on SAM/BAM alignment files.

Complete Stats::

  <STATS>           : mean, max, stdev, median, Q1 (25 percentile), Q3
  reads             : # of entries in the sam file, might not be # reads
  phred             : phred scale used
  bsize             : # reads used for qual stats
  mapped reads      : number of aligned reads (unique probe id sequences)
  mapped bases      : total of the lengths of the aligned reads
  forward           : number of forward-aligned reads
  reverse           : number of reverse-aligned reads
  snp rate          : mismatched bases / total bases
  ins rate          : insert bases / total bases
  del rate          : deleted bases / total bases
  pct mismatch      : percent of reads that have mismatches
  len <STATS>       : read length stats, ignored if fixed-length
  mapq <STATS>      : stats for mapping qualities
  insert <STATS>    : stats for insert sizes
  <CHR>           : percentage of mapped bases per chr, followed by a signature

Subsampled stats (1M reads max)::

  base qual <STATS> : stats for base qualities
  A,T,C,G       : base percentages

Meaning of the per-chromosome signature:

  A ascii-histogram of mapped reads by chromosome position.  It is only output if the original SAM/BAM has a header. The values are the log2 of the # of mapped reads at each position + ascii '0'.

See http://code.google.com/p/ea-utils/wiki/SamStatsDetails for more information on each stat, how it's calculated and what it means.

This tool uses the sam-stats program that is part of the ea-utils suite. See http://code.google.com/p/ea-utils/wiki/SamStats for details.
]]>
    </help>

    <citations>
        <citation type="bibtex">
            @article{aronesty_comparison_2013,
                title = {Comparison of {Sequencing} {Utility} {Programs}},
                volume = {7},
                issn = {18750362},
                url = {http://benthamopen.com/ABSTRACT/TOBIOIJ-7-1},
                doi = {10.2174/1875036201307010001},
                language = {en},
                number = {1},
                urldate = {2015-07-10},
                journal = {The Open Bioinformatics Journal},
                author = {Aronesty, Erik},
                month = jan,
                year = {2013},
                pages = {1--8}
            }
        </citation>
    </citations>

</tool>