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comparison read_quality.xml @ 32:580ee0c4bc4e

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Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc
author lparsons
date Mon, 07 Oct 2013 15:01:13 -0400
parents cc5eaa9376d8
children
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31:cc5eaa9376d8 32:580ee0c4bc4e
1 <tool id="read_quality" name="Read Quality" version="1.1"> 1 <tool id="rseqc_read_quality" name="Read Quality" version="1.1">
2 <description>determines Phred quality score</description> 2 <description>determines Phred quality score</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="2.11.0">R</requirement> 4 <requirement type="package" version="3.0.1">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement> 5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="2.3.7">rseqc</requirement> 6 <requirement type="package" version="2.3.7">rseqc</requirement>
7 </requirements> 7 </requirements>
8 <command> read_quality.py -i $input -o output -r $reduce 8 <command>
9 </command> 9 read_quality.py -i $input -o output -r $reduce
10 <inputs> 10 </command>
11 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
12 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" />
13 </inputs>
14 <outputs>
15 <data format="r" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" />
16 <data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" />
17 <data format="pdf" name="outputpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" />
18 </outputs>
19 <stdio> 11 <stdio>
20 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
21 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
22 </stdio> 14 </stdio>
23 <help> 15 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
17 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" />
18 </inputs>
19 <outputs>
20 <data format="txt" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" />
21 <data format="pdf" name="outputpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" />
22 <data format="pdf" name="outputpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" />
23 </outputs>
24 <help>
24 read_quality.py 25 read_quality.py
25 +++++++++++++++ 26 +++++++++++++++
26 27
27 According to SAM specification, if Q is the character to represent "base calling quality" 28 According to SAM specification, if Q is the character to represent "base calling quality"
28 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that 29 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
35 36
36 Inputs 37 Inputs
37 ++++++++++++++ 38 ++++++++++++++
38 39
39 Input BAM/SAM file 40 Input BAM/SAM file
40 Alignment file in BAM/SAM format. 41 Alignment file in BAM/SAM format.
41 42
42 Ignore phred scores less than this number (default=1000) 43 Ignore phred scores less than this number (default=1000)
43 To avoid making huge vector in R, nucleotide with certain phred score represented less than this number will be ignored. Increase this number save more memory while reduce precision. This option only applies to the 'boxplot'. 44 To avoid making huge vector in R, nucleotide with certain phred score represented less than this number will be ignored. Increase this number save more memory while reduce precision. This option only applies to the 'boxplot'.
44 45
45 Output 46 Output
46 ++++++++++++++ 47 ++++++++++++++
47 48
48 1. output.qual.r 49 1. output.qual.r
71 .. image:: http://rseqc.sourceforge.net/_static/logo.png 72 .. image:: http://rseqc.sourceforge.net/_static/logo.png
72 73
73 .. _RSeQC: http://rseqc.sourceforge.net/ 74 .. _RSeQC: http://rseqc.sourceforge.net/
74 75
75 76
76 </help> 77 </help>
77 </tool> 78 </tool>