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comparison read_duplication.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_duplication" name="Read Duplication" version="1.1"> 1 <tool id="rseqc_read_duplication" name="Read Duplication" version="1.1">
2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</description> 2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</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_duplication.py -i $input -o output -u $upLimit 8 <command>
9 </command> 9 read_duplication.py -i $input -o output -u $upLimit
10 <inputs> 10 </command>
11 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
12 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" />
13 </inputs>
14 <outputs>
15 <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/>
16 <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/>
17 <data format="r" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" />
18 <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
19 </outputs>
20 <stdio> 11 <stdio>
21 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
22 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
23 </stdio> 14 </stdio>
24 <help> 15 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
17 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" />
18 </inputs>
19 <outputs>
20 <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/>
21 <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/>
22 <data format="txt" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" />
23 <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
24 </outputs>
25 <help>
25 read_duplication.py 26 read_duplication.py
26 +++++++++++++++++++ 27 +++++++++++++++++++
27 28
28 Two strategies were used to determine reads duplication rate: 29 Two strategies were used to determine reads duplication rate:
29 30
32 33
33 Inputs 34 Inputs
34 ++++++++++++++ 35 ++++++++++++++
35 36
36 Input BAM/SAM file 37 Input BAM/SAM file
37 Alignment file in BAM/SAM format. 38 Alignment file in BAM/SAM format.
38 39
39 Upper Limit of Plotted Duplicated Times (default=500) 40 Upper Limit of Plotted Duplicated Times (default=500)
40 Only used for plotting. 41 Only used for plotting.
41 42
42 Output 43 Output
43 ++++++++++++++ 44 ++++++++++++++
44 45
45 1. output.dup.pos.DupRate.xls: Read duplication rate determined from mapping position of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads. 46 1. output.dup.pos.DupRate.xls: Read duplication rate determined from mapping position of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
64 .. image:: http://rseqc.sourceforge.net/_static/logo.png 65 .. image:: http://rseqc.sourceforge.net/_static/logo.png
65 66
66 .. _RSeQC: http://rseqc.sourceforge.net/ 67 .. _RSeQC: http://rseqc.sourceforge.net/
67 68
68 69
69 </help> 70 </help>
70 </tool> 71 </tool>