rseqc: read_duplication.xml annotate

annotate read_duplication.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_read_duplication" name="Read Duplication" 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>determines reads duplication rate with sequence-based and mapping-based strategies</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 read_duplication.py -i $input -o output -u $upLimit
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 </command>
31 cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	11 <stdio>
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	12 <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: 24 diff changeset	13 <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: 24 diff changeset	14 </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	15 <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	16 <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	17 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" />
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	18 </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	19 <outputs>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	20 <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	21 <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	22 <data format="txt" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	23 <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (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	24 </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	25 <help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	26 read_duplication.py
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	27 +++++++++++++++++++
24 80f857718ca0 Uploaded nilesh parents: diff changeset	28
31 cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	29 Two strategies were used to determine reads duplication rate:
24 80f857718ca0 Uploaded nilesh parents: diff changeset	30
31 cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	31 * Sequence based: reads with exactly the same sequence content are regarded as duplicated reads.
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	32 * Mapping based: reads mapped to the same genomic location are regarded as duplicated reads. For splice reads, reads mapped to the same starting position and splice the same way are regarded as duplicated reads.
24 80f857718ca0 Uploaded nilesh parents: diff changeset	33
80f857718ca0 Uploaded nilesh parents: diff changeset	34 Inputs
80f857718ca0 Uploaded nilesh parents: diff changeset	35 ++++++++++++++
80f857718ca0 Uploaded nilesh parents: diff changeset	36
80f857718ca0 Uploaded nilesh parents: diff changeset	37 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	38 Alignment file in BAM/SAM format.
24 80f857718ca0 Uploaded nilesh parents: diff changeset	39
80f857718ca0 Uploaded nilesh parents: diff changeset	40 Upper Limit of Plotted Duplicated Times (default=500)
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	41 Only used for plotting.
24 80f857718ca0 Uploaded nilesh parents: diff changeset	42
80f857718ca0 Uploaded nilesh parents: diff changeset	43 Output
80f857718ca0 Uploaded nilesh parents: diff changeset	44 ++++++++++++++
80f857718ca0 Uploaded nilesh parents: diff changeset	45
80f857718ca0 Uploaded nilesh parents: diff changeset	46 1. output.dup.pos.DupRate.xls: Read duplication rate determined from mapping position of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
80f857718ca0 Uploaded nilesh parents: diff changeset	47 2. output.dup.seq.DupRate.xls: Read duplication rate determined from sequence of read. First column is "occurrence" or duplication times, second column is number of uniquely mapped reads.
80f857718ca0 Uploaded nilesh parents: diff changeset	48 3. output.DupRate_plot.r: R script to generate pdf file
80f857718ca0 Uploaded nilesh parents: diff changeset	49 4. output.DupRate_plot.pdf: graphical output generated from R script
80f857718ca0 Uploaded nilesh parents: diff changeset	50
31 cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	51 .. image:: http://rseqc.sourceforge.net/_images/duplicate.png
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	52 :height: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	53 :width: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	54 :scale: 80 %
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	55
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	56 -----
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	57
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	58 About RSeQC
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	59 +++++++++++
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	60
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	61 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: 24 diff changeset	62
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	63 The RSeQC package is licensed under the GNU GPL v3 license.
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	64
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	65 .. image:: http://rseqc.sourceforge.net/_static/logo.png
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	66
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	67 .. _RSeQC: http://rseqc.sourceforge.net/
cc5eaa9376d8 Lance's updates nilesh parents: 24 diff changeset	68
24 80f857718ca0 Uploaded nilesh parents: diff changeset	69
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	70 </help>
24 80f857718ca0 Uploaded nilesh parents: diff changeset	71 </tool>

Mercurial > repos > nilesh > rseqc

annotate read_duplication.xml @ 34:8fbd165f8835