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comparison junction_annotation.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="junction_annotation" name="Junction Annotation" version="1.1"> 1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="1.1">
2 <description>compares detected splice junctions to reference gene model</description> 2 <description>compares detected splice junctions to reference gene model</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> junction_annotation.py -i $input -o output -r $refgene 8 <command>
9 9 junction_annotation.py
10 #if $intron.hasIntron 10 -i $input -o output -r $refgene
11 -m $intron.min_Intron 11 #if $intron.hasIntron
12 #end if 12 -m $intron.min_Intron
13 13 #end if
14 </command> 14 </command>
15 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
17 <param name="refgene" type="data" format="bed" label="reference gene model" />
18 <conditional name="intron">
19 <param name="hasIntron" type="boolean" label="Specify minimum intron length" value="false"/>
20 <when value="true">
21 <param name="min_Intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" />
22 </when>
23 </conditional>
24 </inputs>
25 <outputs>
26 <data format="xls" name="outputxls" from_work_dir="output.junction.xls" label="${tool.name} on ${on_string} (XLS)"/>
27 <data format="r" name="outputr" from_work_dir="output.junction_plot.r" label="${tool.name} on ${on_string} (R Script)" />
28 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events PDF)"/>
29 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction PDF)" />
30 </outputs>
31 <stdio> 15 <stdio>
32 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 16 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
33 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 17 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
34 </stdio> 18 </stdio>
35 <help> 19 <inputs>
20 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
21 <param name="refgene" type="data" format="bed" label="reference gene model" />
22 <conditional name="intron">
23 <param name="hasIntron" type="boolean" label="Specify minimum intron length" value="false"/>
24 <when value="true">
25 <param name="min_Intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" />
26 </when>
27 </conditional>
28 </inputs>
29 <outputs>
30 <data format="xls" name="outputxls" from_work_dir="output.junction.xls" label="${tool.name} on ${on_string} (XLS)"/>
31 <data format="txt" name="outputr" from_work_dir="output.junction_plot.r" label="${tool.name} on ${on_string} (R Script)" />
32 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events PDF)"/>
33 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction PDF)" />
34 </outputs>
35 <help>
36 junction_annotation.py 36 junction_annotation.py
37 ++++++++++++++++++++++ 37 ++++++++++++++++++++++
38 38
39 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED 39 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED
40 format, this program will compare detected splice junctions to reference gene model. splicing 40 format, this program will compare detected splice junctions to reference gene model. splicing
52 52
53 Inputs 53 Inputs
54 ++++++++++++++ 54 ++++++++++++++
55 55
56 Input BAM/SAM file 56 Input BAM/SAM file
57 Alignment file in BAM/SAM format. 57 Alignment file in BAM/SAM format.
58 58
59 Reference gene model 59 Reference gene model
60 Gene model in BED format. 60 Gene model in BED format.
61 61
62 Minimum intron length (default=50) 62 Minimum intron length (default=50)
63 Minimum intron length (bp). 63 Minimum intron length (bp).
64 64
65 65
66 Output 66 Output
67 ++++++++++++++ 67 ++++++++++++++
68 68
95 .. _RSeQC: http://rseqc.sourceforge.net/ 95 .. _RSeQC: http://rseqc.sourceforge.net/
96 96
97 97
98 98
99 99
100 </help> 100 </help>
101 </tool> 101 </tool>