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comparison bam_stat.xml @ 49:6b33e31bda10 draft

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Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
author lparsons
date Thu, 16 Jul 2015 17:43:43 -0400
parents eb339c5849bb
children 09846d5169fa
comparison
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48:2e6190c29c54 49:6b33e31bda10
1 <tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="2.4"> 1 <tool id="rseqc_bam_stat" name="BAM/SAM Mapping Stats" version="2.4galaxy1">
2 <description> 2 <description>
3 reads mapping statistics for a provided BAM or SAM file. 3 reads mapping statistics for a provided BAM or SAM file.
4 </description> 4 </description>
5
6 <macros>
7 <import>rseqc_macros.xml</import>
8 </macros>
9
5 <requirements> 10 <requirements>
6 <requirement type="package" version="1.7.1">numpy</requirement> 11 <expand macro="requirement_package_numpy" />
7 <requirement type="package" version="2.4">rseqc</requirement> 12 <expand macro="requirement_package_rseqc" />
8 </requirements>s 13 </requirements>
9 <command> 14
10 bam_stat.py -i $input -q $mapqual 2> $output 15 <expand macro="stdio" />
16
17 <version_command><![CDATA[bam_stat.py --version]]></version_command>
18
19 <command><![CDATA[
20 bam_stat.py -i $input -q $mapq 2> $output
21 ]]>
11 </command> 22 </command>
12 <stdio> 23
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> 24 <inputs>
17 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" /> 25 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
18 <param label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" /> 26 <param name="mapq" value="30" type="integer" label="Minimum mapping quality for an alignment to be called 'uniquly mapped'" help="(--mapq)" />
19 </inputs> 27 </inputs>
28
20 <outputs> 29 <outputs>
21 <data format="txt" name="output" /> 30 <data format="txt" name="output" />
22 </outputs> 31 </outputs>
23 <help> 32
33 <tests>
34 <test>
35 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
36 <output name="output" file="bamstats.txt"/>
37 </test>
38 </tests>
39
40 <help><![CDATA[
24 bam_stat.py 41 bam_stat.py
25 +++++++++++ 42 +++++++++++
26 43
27 This program is used to calculate reads mapping statistics from provided BAM 44 This program is used to calculate reads mapping statistics from provided BAM
28 file. This script determines "uniquely mapped reads" from `mapping quality`_, 45 file. This script determines "uniquely mapped reads" from `mapping quality
46 <http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores>`_,
29 which quality the probability that a read is misplaced (Do NOT confused with 47 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 48 sequence quality, sequence quality measures the probability that a base-calling
31 was wrong) . 49 was wrong) .
32 50
33 Inputs 51 Inputs
35 53
36 Input BAM/SAM file 54 Input BAM/SAM file
37 Alignment file in BAM/SAM format. 55 Alignment file in BAM/SAM format.
38 56
39 Minimum mapping quality 57 Minimum mapping quality
40 Minimum mapping quality for an alignment to be called “uniquely mapped” (default=30) 58 Minimum mapping quality for an alignment to be called "uniquely mapped" (default=30)
41 59
42 Output 60 Output
43 ++++++++++++++ 61 ++++++++++++++
44 62
45 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped} 63 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
47 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'} 65 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
48 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads} 66 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
49 67
50 ----- 68 -----
51 69
52 About RSeQC 70 About RSeQC
53 +++++++++++ 71 +++++++++++
72
54 73
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. 74 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 75
57 The RSeQC package is licensed under the GNU GPL v3 license. 76 The RSeQC package is licensed under the GNU GPL v3 license.
58 77
59 .. image:: http://rseqc.sourceforge.net/_static/logo.png 78 .. image:: http://rseqc.sourceforge.net/_static/logo.png
60 79
61 .. _RSeQC: http://rseqc.sourceforge.net/ 80 .. _RSeQC: http://rseqc.sourceforge.net/
62 .. _`mapping quality`: http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores
63 81
82 ]]>
64 </help> 83 </help>
84
85 <expand macro="citations" />
65 </tool> 86 </tool>