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comparison geneBody_coverage2.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="geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="1.1"> 1 <tool id="rseqc_geneBody_coverage2" name="Gene Body Converage (Bigwig)" version="1.1">
2 <description> 2 <description>
3 Read coverage over gene body. 3 Read coverage over gene body
4 </description> 4 </description>
5 <requirements> 5 <requirements>
6 <requirement type="package" version="2.11.0">R</requirement> 6 <requirement type="package" version="3.0.1">R</requirement>
7 <requirement type="package" version="1.7.1">numpy</requirement> 7 <requirement type="package" version="1.7.1">numpy</requirement>
8 <requirement type="package" version="2.3.7">rseqc</requirement> 8 <requirement type="package" version="2.3.7">rseqc</requirement>
9 </requirements> 9 </requirements>
10 <command> 10 <command>
11 geneBody_coverage2.py -i $input -r $refgene -o output 11 geneBody_coverage2.py -i $input -r $refgene -o output
12 </command> 12 </command>
13 <inputs>
14 <param name="input" type="data" label="Input bigwig file" format="bigwig" />
15 <param name="refgene" type="data" label="Reference Genome" format="bed" />
16 </inputs>
17 <outputs>
18 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" />
19 <data name="outputr" format="r" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" />
20 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
21 </outputs>
22 <stdio> 13 <stdio>
23 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 14 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
24 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 15 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
25 </stdio> 16 </stdio>
26 <help> 17 <inputs>
18 <param name="input" type="data" label="Input bigwig file" format="bigwig" />
19 <param name="refgene" type="data" label="Reference Genome" format="bed" />
20 </inputs>
21 <outputs>
22 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" />
23 <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" />
24 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
25 </outputs>
26 <help>
27 geneBody_coverage2.py 27 geneBody_coverage2.py
28 +++++++++++++++++++++ 28 +++++++++++++++++++++
29 29
30 Similar to geneBody_coverage.py. This module takes bigwig instead of BAM as input, and thus 30 Similar to geneBody_coverage.py. This module takes bigwig instead of BAM as input, and thus
31 requires much less memory. The BigWig file could be arbitrarily large. 31 requires much less memory. The BigWig file could be arbitrarily large.
33 33
34 Inputs 34 Inputs
35 ++++++++++++++ 35 ++++++++++++++
36 36
37 Input BAM/SAM file 37 Input BAM/SAM file
38 Alignment file in BAM/SAM format. 38 Alignment file in BAM/SAM format.
39 39
40 Reference gene model 40 Reference gene model
41 Gene Model in BED format. 41 Gene Model in BED format.
42 42
43 43
44 Outputs 44 Outputs
45 ++++++++++++++ 45 ++++++++++++++
46 46
65 65
66 .. _RSeQC: http://rseqc.sourceforge.net/ 66 .. _RSeQC: http://rseqc.sourceforge.net/
67 67
68 68
69 69
70 </help> 70 </help>
71 </tool> 71 </tool>