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comparison geneBody_coverage.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_coverage" name="Gene Body Converage (BAM)" version="1.1"> 1 <tool id="rseqc_geneBody_coverage" name="Gene Body Converage (BAM)" 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_coverage.py -i $input -r $refgene -o output 11 geneBody_coverage.py -i $input -r $refgene -o output
12 </command> 12 </command>
13 <inputs>
14 <param name="input" type="data" label="Input .bam file" format="bam" />
15 <param name="refgene" type="data" label="Reference Genome" format="bed" />
16 </inputs>
17 <outputs>
18 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${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 ${on_string} (Text)" />
21 </outputs>
22 <stdio> 13 <stdio>
23 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 14 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
24 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 15 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
25 </stdio> 16 </stdio>
26 <help> 17 <inputs>
18 <param name="input" type="data" label="Input .bam file" format="bam" />
19 <param name="refgene" type="data" label="Reference Genome" format="bed" />
20 </inputs>
21 <outputs>
22 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${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_coverage.py 27 geneBody_coverage.py
28 ++++++++++++++++++++ 28 ++++++++++++++++++++
29 29
30 Read coverage over gene body. This module is used to check if reads coverage is uniform and 30 Read coverage over gene body. This module is used to check if reads coverage is uniform and
31 if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the 31 if there is any 5\'/3\' bias. This module scales all transcripts to 100 nt and calculates the
52 52
53 Example output: 53 Example output:
54 .. image:: http://rseqc.sourceforge.net/_images/geneBody_coverage.png 54 .. image:: http://rseqc.sourceforge.net/_images/geneBody_coverage.png
55 :height: 600 px 55 :height: 600 px
56 :width: 600 px 56 :width: 600 px
57 :scale: 80 % 57 :scale: 80 %
58 58
59 59
60 ----- 60 -----
61 61
62 About RSeQC 62 About RSeQC