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comparison junction_saturation.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_saturation" name="Junction Saturation" version="1.1"> 1 <tool id="rseqc_junction_saturation" name="Junction Saturation" version="1.1">
2 <description>detects splice junctions from each subset and compares them to reference gene model</description> 2 <description>detects splice junctions from each subset and compares them 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_saturation.py -i $input -o output -r $refgene -m $intronSize -v $minSplice 8 <command> junction_saturation.py -i $input -o output -r $refgene -m $intronSize -v $minSplice
9 9
10 #if $percentiles.specifyPercentiles 10 #if $percentiles.specifyPercentiles
11 -l $percentiles.lowBound -u $percentiles.upBound -s $percentiles.percentileStep 11 -l $percentiles.lowBound -u $percentiles.upBound -s $percentiles.percentileStep
12 #end if 12 #end if
13 13
14 </command> 14 </command>
15 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
17 <param name="refgene" type="data" format="bed" label="reference gene model" />
18 <param name="intronSize" type="integer" label="Minimum intron size (bp, default=50)" value="50"/>
19 <param name="minSplice" type="integer" label="Minimum coverage (default=1)" value="1" />
20 <conditional name="percentiles">
21 <param name="specifyPercentiles" type="boolean" label="Specify sampling bounds and frequency" value="false"/>
22 <when value="true">
23 <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" />
24 <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" />
25 <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" />
26 </when>
27 </conditional>
28 </inputs>
29 <outputs>
30 <data format="r" name="outputr" from_work_dir="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string} (R Script)"/>
31 <data format="pdf" name="outputpdf" from_work_dir="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string} (PDF)"/>
32 </outputs>
33 <stdio> 15 <stdio>
34 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" /> 16 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
35 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" /> 17 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
36 </stdio> 18 </stdio>
37 <help> 19 <inputs>
20 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
21 <param name="refgene" type="data" format="bed" label="reference gene model" />
22 <param name="intronSize" type="integer" label="Minimum intron size (bp, default=50)" value="50"/>
23 <param name="minSplice" type="integer" label="Minimum coverage (default=1)" value="1" />
24 <conditional name="percentiles">
25 <param name="specifyPercentiles" type="boolean" label="Specify sampling bounds and frequency" value="false"/>
26 <when value="true">
27 <param name="lowBound" type="integer" value="5" label="Lower Bound Sampling Frequency (bp, default=5)" />
28 <param name="upBound" type="integer" value="100" label="Upper Bound Sampling Frequency (bp, default=100)" />
29 <param name="percentileStep" type="integer" value="5" label="Sampling increment (default=5)" />
30 </when>
31 </conditional>
32 </inputs>
33 <outputs>
34 <data format="txt" name="outputr" from_work_dir="output.junctionSaturation_plot.r" label="${tool.name} on ${on_string} (R Script)"/>
35 <data format="pdf" name="outputpdf" from_work_dir="output.junctionSaturation_plot.pdf" label="${tool.name} on ${on_string} (PDF)"/>
36 </outputs>
37 <help>
38 junction_saturation.py 38 junction_saturation.py
39 ++++++++++++++++++++++ 39 ++++++++++++++++++++++
40 40
41 It's very important to check if current sequencing depth is deep enough to perform 41 It's very important to check if current sequencing depth is deep enough to perform
42 alternative splicing analyses. For a well annotated organism, the number of expressed genes 42 alternative splicing analyses. For a well annotated organism, the number of expressed genes
50 50
51 Inputs 51 Inputs
52 ++++++++++++++ 52 ++++++++++++++
53 53
54 Input BAM/SAM file 54 Input BAM/SAM file
55 Alignment file in BAM/SAM format. 55 Alignment file in BAM/SAM format.
56 56
57 Reference gene model 57 Reference gene model
58 Gene model in BED format. 58 Gene model in BED format.
59 59
60 Sampling Percentiles - Upper Bound, Lower Bound, Sampling Increment (defaults= 100, 5, and 5) 60 Sampling Percentiles - Upper Bound, Lower Bound, Sampling Increment (defaults= 100, 5, and 5)
61 Sampling starts from the Lower Bound and increments to the Upper Bound at the rate of the Sampling Increment. 61 Sampling starts from the Lower Bound and increments to the Upper Bound at the rate of the Sampling Increment.
62 62
63 Minimum intron length (default=50) 63 Minimum intron length (default=50)
64 Minimum intron length (bp). 64 Minimum intron length (bp).
65 65
66 Minimum coverage (default=1) 66 Minimum coverage (default=1)
67 Minimum number of supportting reads to call a junction. 67 Minimum number of supportting reads to call a junction.
68 68
69 Output 69 Output
70 ++++++++++++++ 70 ++++++++++++++
71 71
72 1. output.junctionSaturation_plot.r: R script to generate plot 72 1. output.junctionSaturation_plot.r: R script to generate plot
93 93
94 .. _RSeQC: http://rseqc.sourceforge.net/ 94 .. _RSeQC: http://rseqc.sourceforge.net/
95 95
96 96
97 97
98 </help> 98 </help>
99 </tool> 99 </tool>