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comparison read_distribution.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_distribution" name="Read Distribution" version="1.1"> 1 <tool id="rseqc_read_distribution" name="Read Distribution" version="1.1">
2 <description>calculates how mapped reads were distributed over genome feature</description> 2 <description>calculates how mapped reads were distributed over genome feature</description>
3 <requirements> 3 <requirements>
4 <requirement type="package" version="1.7.1">numpy</requirement> 4 <requirement type="package" version="1.7.1">numpy</requirement>
5 <requirement type="package" version="2.3.7">rseqc</requirement> 5 <requirement type="package" version="2.3.7">rseqc</requirement>
6 </requirements> 6 </requirements>
7 <command> read_distribution.py -i $input -r $refgene > $output 7 <command>
8 </command> 8 read_distribution.py -i $input -r $refgene > $output
9 <inputs> 9 </command>
10 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
11 <param name="refgene" type="data" format="bed" label="reference gene model" />
12 </inputs>
13 <outputs>
14 <data format="txt" name="output" />
15 </outputs>
16 <stdio> 10 <stdio>
17 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 11 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
18 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 12 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
19 </stdio> 13 </stdio>
20 <help> 14 <inputs>
15 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
16 <param name="refgene" type="data" format="bed" label="reference gene model" />
17 </inputs>
18 <outputs>
19 <data format="txt" name="output" />
20 </outputs>
21 <help>
21 read_distribution.py 22 read_distribution.py
22 ++++++++++++++++++++ 23 ++++++++++++++++++++
23 24
24 Provided a BAM/SAM file and reference gene model, this module will calculate how mapped 25 Provided a BAM/SAM file and reference gene model, this module will calculate how mapped
25 reads were distributed over genome feature (like CDS exon, 5'UTR exon, 3' UTR exon, Intron, 26 reads were distributed over genome feature (like CDS exon, 5'UTR exon, 3' UTR exon, Intron,
43 44
44 Inputs 45 Inputs
45 ++++++++++++++ 46 ++++++++++++++
46 47
47 Input BAM/SAM file 48 Input BAM/SAM file
48 Alignment file in BAM/SAM format. 49 Alignment file in BAM/SAM format.
49 50
50 Reference gene model 51 Reference gene model
51 Gene model in BED format. 52 Gene model in BED format.
52 53
53 Sample Output 54 Sample Output
54 ++++++++++++++ 55 ++++++++++++++
55 56
56 Output: 57 Output:
83 84
84 .. _RSeQC: http://rseqc.sourceforge.net/ 85 .. _RSeQC: http://rseqc.sourceforge.net/
85 86
86 87
87 88
88 </help> 89 </help>
89 </tool> 90 </tool>