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comparison bam_stat.xml @ 45:eb339c5849bb draft

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Reupload, toolshed removed all files of previous version.
author lparsons
date Fri, 26 Sep 2014 15:04:18 -0400
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44:20e0b2dd7882 45:eb339c5849bb
1 <tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="2.4">
2 <description>
3 reads mapping statistics for a provided BAM or SAM file.
4 </description>
5 <requirements>
6 <requirement type="package" version="1.7.1">numpy</requirement>
7 <requirement type="package" version="2.4">rseqc</requirement>
8 </requirements>s
9 <command>
10 bam_stat.py -i $input -q $mapqual 2> $output
11 </command>
12 <stdio>
13 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
14 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
15 </stdio>
16 <inputs>
17 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
18 <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" />
19 </inputs>
20 <outputs>
21 <data format="txt" name="output" />
22 </outputs>
23 <help>
24 bam_stat.py
25 +++++++++++
26
27 This program is used to calculate reads mapping statistics from provided BAM
28 file. This script determines "uniquely mapped reads" from `mapping quality`_,
29 which quality the probability that a read is misplaced (Do NOT confused with
30 sequence quality, sequence quality measures the probability that a base-calling
31 was wrong) .
32
33 Inputs
34 ++++++++++++++
35
36 Input BAM/SAM file
37 Alignment file in BAM/SAM format.
38
39 Minimum mapping quality
40 Minimum mapping quality for an alignment to be called “uniquely mapped” (default=30)
41
42 Output
43 ++++++++++++++
44
45 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
46 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
47 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
48 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
49
50 -----
51
52 About RSeQC
53 +++++++++++
54
55 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
56
57 The RSeQC package is licensed under the GNU GPL v3 license.
58
59 .. image:: http://rseqc.sourceforge.net/_static/logo.png
60
61 .. _RSeQC: http://rseqc.sourceforge.net/
62 .. _`mapping quality`: http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores
63
64 </help>
65 </tool>