Mercurial > repos > lparsons > sam_stats

comparison sam-stats.xml @ 0:b9e7569a4438 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded initial version with package dependency.
author lparsons
date Fri, 27 Jun 2014 15:36:01 -0400
parents
children a51942c74761
comparison
equal deleted inserted replaced
-1:000000000000 0:b9e7569a4438
1 <tool id="sam_stats" name="sam-stats" version="1.32">
2 <description> - Compute statistics from SAM or BAM files</description>
3 <requirements>
4 <requirement type="package" version="1.1.2-484">ea-utils</requirement>
5 </requirements>
6 <command>
7 sam-stats
8 $trackMultAlign
9 $reportAllChr
10 #if $rnaSeqStats:
11 -R $rnaSeqStatsFile
12 #end if
13 #if $input.extension == "bam":
14 -B
15 #end if
16 -S $histBinSize
17 $input
18 &gt; $samStats
19 </command>
20 <inputs>
21 <param format="sam,bam" name="input" type="data" label="SAM/BAM File" />
22 <param name="trackMultAlign" type="boolean" value="False" truevalue="-D" falsevalue="" label="Keep track of multiple alignments (slower!)" />
23 <param name="reportAllChr" type="boolean" value="False" truevalue="-A" falsevalue="" label="Report all chr sigs, even if there are more than 1000" />
24 <!-- <param name="numReadsSubsample" type="integer" value="1000000" min="1" max="1000000" label="Number of reads to sample for per-base statistics (max 1,000,000)" /> -->
25 <param name="histBinSize" type="integer" value="30" min="1" label="Number of bins per chromosome for reads by chromosome &quot;histogram&quot;" />
26 <param name="rnaSeqStats" type="boolean" value="False" label="Output RNA-Seq statistics (coverage, 3 prime bias, etc.)" />
27 </inputs>
28
29 <outputs>
30 <data format="tabular" name="samStats" label="${tool.name} on ${on_string}"/>
31 <data format="tabular" name="rnaSeqStatsFile" label="${tool.name} on ${on_string} (RNA-Seq Stats)"> <filter>rnaSeqStats</filter>
32 </data>
33 </outputs>
34
35 <stdio>
36 <exit_code range="1:" level="fatal" description="Unknown error occurred" />
37 </stdio>
38
39 <tests>
40 <test>
41 <param name="input" value="test.sam" />
42 <output name="samStats" file="testout.txt" />
43 </test>
44 </tests>
45
46 <help>
47 Overview
48 --------
49 sam-stats computes varius statics on SAM/BAM alignment files.
50
51 Complete Stats::
52
53 &lt;STATS&gt; : mean, max, stdev, median, Q1 (25 percentile), Q3
54 reads : # of entries in the sam file, might not be # reads
55 phred : phred scale used
56 bsize : # reads used for qual stats
57 mapped reads : number of aligned reads (unique probe id sequences)
58 mapped bases : total of the lengths of the aligned reads
59 forward : number of forward-aligned reads
60 reverse : number of reverse-aligned reads
61 snp rate : mismatched bases / total bases
62 ins rate : insert bases / total bases
63 del rate : deleted bases / total bases
64 pct mismatch : percent of reads that have mismatches
65 len &lt;STATS&gt; : read length stats, ignored if fixed-length
66 mapq &lt;STATS&gt; : stats for mapping qualities
67 insert &lt;STATS&gt; : stats for insert sizes
68 &lt;CHR&gt; : percentage of mapped bases per chr, followed by a signature
69
70 Subsampled stats (1M reads max)::
71
72 base qual &lt;STATS&gt; : stats for base qualities
73 A,T,C,G : base percentages
74
75 Meaning of the per-chromosome signature:
76
77 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'.
78
79 See http://code.google.com/p/ea-utils/wiki/SamStatsDetails for more information on each stat, how it's calculated and what it means.
80
81 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.
82 </help>
83 </tool>