rseqc: junction_annotation.xml annotate

annotate junction_annotation.xml @ 34:8fbd165f8835

Patch from Bjorn Gruning

author	lparsons
date	Mon, 04 Nov 2013 16:19:36 -0500
parents	580ee0c4bc4e
children

rev	line source
32 580ee0c4bc4e 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 lparsons parents: 31 diff changeset	1 <tool id="rseqc_junction_annotation" name="Junction Annotation" version="1.1">
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	2 <description>compares detected splice junctions to reference gene model</description>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	3 <requirements>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	4 <requirement type="package" version="3.0.1">R</requirement>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	5 <requirement type="package" version="1.7.1">numpy</requirement>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	6 <requirement type="package" version="2.3.7">rseqc</requirement>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	7 </requirements>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	8 <command>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	9 junction_annotation.py
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	10 -i $input -o output -r $refgene
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	11 #if $intron.hasIntron
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	12 -m $intron.min_Intron
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	13 #end if
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	14 </command>
31 cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	15 <stdio>
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	16 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	17 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	18 </stdio>
32 580ee0c4bc4e 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 lparsons parents: 31 diff changeset	19 <inputs>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	20 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	21 <param name="refgene" type="data" format="bed" label="reference gene model" />
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	22 <conditional name="intron">
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	23 <param name="hasIntron" type="boolean" label="Specify minimum intron length" value="false"/>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	24 <when value="true">
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	25 <param name="min_Intron" type="integer" value="50" label="Minimum intron length (bp, default=50)" />
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	26 </when>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	27 </conditional>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	28 </inputs>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	29 <outputs>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	30 <data format="xls" name="outputxls" from_work_dir="output.junction.xls" label="${tool.name} on ${on_string} (XLS)"/>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	31 <data format="txt" name="outputr" from_work_dir="output.junction_plot.r" label="${tool.name} on ${on_string} (R Script)" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	32 <data format="pdf" name="outputpdf" from_work_dir="output.splice_events.pdf" label="${tool.name} on ${on_string} (Splice Events PDF)"/>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	33 <data format="pdf" name="outputjpdf" from_work_dir="output.splice_junction.pdf" label="${tool.name} on ${on_string} (Splice Junction PDF)" />
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	34 </outputs>
580ee0c4bc4e 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 lparsons parents: 31 diff changeset	35 <help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	36 junction_annotation.py
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	37 ++++++++++++++++++++++
21 93c0e1cc65c6 Uploaded nilesh parents: diff changeset	38
31 cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	39 For a given alignment file (-i) in BAM or SAM format and a reference gene model (-r) in BED
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	40 format, this program will compare detected splice junctions to reference gene model. splicing
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	41 annotation is performed in two levels: splice event level and splice junction level.
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	42
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	43 * splice event: An RNA read, especially long read, can be spliced 2 or more times, each time is called a splicing event; In this sense, 100 spliced reads can produce >= 100 splicing events.
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	44 * splice junction: multiple splicing events spanning the same intron can be consolidated into one splicing junction.
21 93c0e1cc65c6 Uploaded nilesh parents: diff changeset	45
31 cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	46 All detected junctions can be grouped to 3 exclusive categories:
21 93c0e1cc65c6 Uploaded nilesh parents: diff changeset	47
31 cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	48 1. Annotated: The junction is part of the gene model. Both splice sites, 5' splice site
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	49 (5'SS) and 3'splice site (3'SS) can be annotated by reference gene model.
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	50 2. complete_novel: Complete new junction. Neither of the two splice sites cannot be annotated by gene model
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	51 3. partial_novel: One of the splice site (5'SS or 3'SS) is new, while the other splice site is annotated (known)
21 93c0e1cc65c6 Uploaded nilesh parents: diff changeset	52
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	53 Inputs
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	54 ++++++++++++++
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	55
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	56 Input BAM/SAM file
32 580ee0c4bc4e 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 lparsons parents: 31 diff changeset	57 Alignment file in BAM/SAM format.
21 93c0e1cc65c6 Uploaded nilesh parents: diff changeset	58
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	59 Reference gene model
32 580ee0c4bc4e 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 lparsons parents: 31 diff changeset	60 Gene model in BED format.
21 93c0e1cc65c6 Uploaded nilesh parents: diff changeset	61
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	62 Minimum intron length (default=50)
32 580ee0c4bc4e 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 lparsons parents: 31 diff changeset	63 Minimum intron length (bp).
21 93c0e1cc65c6 Uploaded nilesh parents: diff changeset	64
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	65
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	66 Output
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	67 ++++++++++++++
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	68
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	69 1. output.junc.anno.junction.xls:
31 cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	70 - chrom ID
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	71 - start position of junction (coordinate is 0 based)
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	72 - end position of junction (coordinate is 1 based)
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	73 - number of splice events supporting this junction
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	74 - 'annotated', 'complete_novel' or 'partial_novel'.
21 93c0e1cc65c6 Uploaded nilesh parents: diff changeset	75 2. output.anno.junction_plot.r: R script to generate pie chart
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	76 3. output.splice_junction.pdf: plot of splice junctions
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	77 4. output.splice_events.pdf: plot of splice events
31 cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	78
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	79 .. image:: http://rseqc.sourceforge.net/_images/junction.png
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	80 :height: 400 px
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	81 :width: 850 px
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	82 :scale: 80 %
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	83
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	84 -----
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	85
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	86 About RSeQC
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	87 +++++++++++
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	88
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	89 The RSeQC_ package provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. "Basic modules" quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while "RNA-seq specific modules" investigate sequencing saturation status of both splicing junction detection and expression estimation, mapped reads clipping profile, mapped reads distribution, coverage uniformity over gene body, reproducibility, strand specificity and splice junction annotation.
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	90
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	91 The RSeQC package is licensed under the GNU GPL v3 license.
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	92
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	93 .. image:: http://rseqc.sourceforge.net/_static/logo.png
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	94
cc5eaa9376d8 Lance's updates nilesh parents: 21 diff changeset	95 .. _RSeQC: http://rseqc.sourceforge.net/
21 93c0e1cc65c6 Uploaded nilesh parents: diff changeset	96
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	97
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	98
93c0e1cc65c6 Uploaded nilesh parents: diff changeset	99
32 580ee0c4bc4e 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 lparsons parents: 31 diff changeset	100 </help>
21 93c0e1cc65c6 Uploaded nilesh parents: diff changeset	101 </tool>

Mercurial > repos > nilesh > rseqc

annotate junction_annotation.xml @ 34:8fbd165f8835