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comparison read_quality.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 f242ee103277
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48:2e6190c29c54 49:6b33e31bda10
1 <tool id="rseqc_read_quality" name="Read Quality" version="2.4"> 1 <tool id="rseqc_read_quality" name="Read Quality" version="2.4galaxy1">
2 <description>determines Phred quality score</description> 2 <description>determines Phred quality score</description>
3
4 <macros>
5 <import>rseqc_macros.xml</import>
6 </macros>
7
3 <requirements> 8 <requirements>
4 <requirement type="package" version="3.0.3">R</requirement> 9 <expand macro="requirement_package_r" />
5 <requirement type="package" version="1.7.1">numpy</requirement> 10 <expand macro="requirement_package_numpy" />
6 <requirement type="package" version="2.4">rseqc</requirement> 11 <expand macro="requirement_package_rseqc" />
7 </requirements> 12 </requirements>
8 <command> 13
9 read_quality.py -i $input -o output -r $reduce 14 <expand macro="stdio" />
15
16 <version_command><![CDATA[read_quality.py --version]]></version_command>
17
18 <command><![CDATA[
19 read_quality.py
20 --input-file $input
21 --out-prefix output
22 -r $reduce
23 --mapq $mapq
24 ]]>
10 </command> 25 </command>
11 <stdio> 26
12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
14 </stdio>
15 <inputs> 27 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> 28 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
17 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" /> 29 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
30 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
18 </inputs> 31 </inputs>
32
19 <outputs> 33 <outputs>
20 <data format="txt" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" /> 34 <data format="txt" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" />
21 <data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" /> 35 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" />
22 <data format="pdf" name="outputpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" /> 36 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" />
23 </outputs> 37 </outputs>
24 <help> 38
39 <!-- Unable to succefully run this script with test data
40 <tests>
41 <test>
42 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig"/>
43 <output name="outputr" file="output.qual.r"/>
44 <output name="outputheatpdf" file="output.qual.heatmap.pdf"/>
45 <output name="outputboxpdf" file="output.qual.boxplot.pdf"/>
46 </test>
47 </tests>
48 -->
49
50 <help><![CDATA[
25 read_quality.py 51 read_quality.py
26 +++++++++++++++ 52 +++++++++++++++
27 53
28 According to SAM specification, if Q is the character to represent "base calling quality" 54 According to SAM specification, if Q is the character to represent "base calling quality"
29 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that 55 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
30 returns an integer representing the Unicode code point of the character when the argument 56 returns an integer representing the Unicode code point of the character when the argument
31 is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used 57 is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used
32 to measure "reliability" of base-calling, for example, phred quality score of 20 means 58 to measure "reliability" of base-calling, for example, phred quality score of 20 means
33 there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there 59 there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there
34 is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P, 60 is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P,
35 here P is probability that base-calling is wrong. 61 here P is probability that base-calling is wrong.
36 62
37 Inputs 63 Inputs
38 ++++++++++++++ 64 ++++++++++++++
49 1. output.qual.r 75 1. output.qual.r
50 2. output.qual.boxplot.pdf 76 2. output.qual.boxplot.pdf
51 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.plot.png 77 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.plot.png
52 :height: 600 px 78 :height: 600 px
53 :width: 600 px 79 :width: 600 px
54 :scale: 80 % 80 :scale: 80 %
55 3. output.qual.heatmap.pdf 81 3. output.qual.heatmap.pdf
56 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.heatmap.png 82 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.heatmap.png
57 :height: 600 px 83 :height: 600 px
58 :width: 600 px 84 :width: 600 px
59 :scale: 80 % 85 :scale: 80 %
60 86
61 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density") 87 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")
62 88
63 ----- 89 -----
64 90
65 About RSeQC 91 About RSeQC
66 +++++++++++ 92 +++++++++++
67 93
68 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. 94 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.
69 95
70 The RSeQC package is licensed under the GNU GPL v3 license. 96 The RSeQC package is licensed under the GNU GPL v3 license.
71 97
72 .. image:: http://rseqc.sourceforge.net/_static/logo.png 98 .. image:: http://rseqc.sourceforge.net/_static/logo.png
73 99
74 .. _RSeQC: http://rseqc.sourceforge.net/ 100 .. _RSeQC: http://rseqc.sourceforge.net/
101 ]]>
102 </help>
75 103
104 <expand macro="citations" />
76 105
77 </help>
78 </tool> 106 </tool>