Mercurial > repos > lparsons > ea_utils

comparison sam-stats.xml @ 1:cf4b5125a835 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author lparsons
date Tue, 20 Nov 2012 15:54:14 -0500
parents
children
comparison
equal deleted inserted replaced
0:e6f1c31279db 1:cf4b5125a835
1 <tool id="sam_stats" name="sam-stats" version="0.1">
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>