rseqc: geneBody_coverage2.xml annotate

annotate geneBody_coverage2.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_geneBody_coverage2" name="Gene Body Converage (Bigwig)" 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>
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 Read coverage over gene body
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 </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	5 <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	6 <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	7 <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	8 <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	9 </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	10 <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	11 geneBody_coverage2.py -i $input -r $refgene -o output
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 </command>
31 cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	13 <stdio>
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	14 <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: 18 diff changeset	15 <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: 18 diff changeset	16 </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	17 <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	18 <param name="input" type="data" label="Input bigwig file" format="bigwig" />
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 <param name="refgene" type="data" label="Reference Genome" format="bed" />
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 </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	21 <outputs>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	22 <data name="outputpdf" format="pdf" from_work_dir="output.geneBodyCoverage.pdf" label="${tool.name} on ${on_string} (PDF)" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	23 <data name="outputr" format="txt" from_work_dir="output.geneBodyCoverage_plot.r" label="${tool.name} on ${on_string} (R Script)" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	24 <data name="outputtxt" format="txt" from_work_dir="output.geneBodyCoverage.txt" label="${tool.name} on ${on_string} (Text)" />
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 </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	26 <help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	27 geneBody_coverage2.py
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	28 +++++++++++++++++++++
18 64dc986da596 Uploaded nilesh parents: diff changeset	29
31 cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	30 Similar to geneBody_coverage.py. This module takes bigwig instead of BAM as input, and thus
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	31 requires much less memory. The BigWig file could be arbitrarily large.
18 64dc986da596 Uploaded nilesh parents: diff changeset	32
64dc986da596 Uploaded nilesh parents: diff changeset	33
64dc986da596 Uploaded nilesh parents: diff changeset	34 Inputs
64dc986da596 Uploaded nilesh parents: diff changeset	35 ++++++++++++++
64dc986da596 Uploaded nilesh parents: diff changeset	36
64dc986da596 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.
18 64dc986da596 Uploaded nilesh parents: diff changeset	39
64dc986da596 Uploaded nilesh parents: diff changeset	40 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	41 Gene Model in BED format.
18 64dc986da596 Uploaded nilesh parents: diff changeset	42
64dc986da596 Uploaded nilesh parents: diff changeset	43
64dc986da596 Uploaded nilesh parents: diff changeset	44 Outputs
64dc986da596 Uploaded nilesh parents: diff changeset	45 ++++++++++++++
64dc986da596 Uploaded nilesh parents: diff changeset	46
64dc986da596 Uploaded nilesh parents: diff changeset	47 Read coverage over gene body. This module is used to check if reads coverage is uniform and if there is any 5’/3’ bias. This module scales all transcripts to 100 nt and calculates the number of reads covering each nucleotide position. Finally, it generates a plot illustrating the coverage profile along the gene body. NOTE: this module requires lots of memory for large BAM files, because it load the entire BAM file into memory. We add another script "geneBody_coverage2.py" into v2.3.1 which takes bigwig (instead of BAM) as input. It only use 200M RAM, but users need to convert BAM into WIG, and then WIG into BigWig.
64dc986da596 Uploaded nilesh parents: diff changeset	48
64dc986da596 Uploaded nilesh parents: diff changeset	49 Example output:
31 cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	50 .. image:: http://dldcc-web.brc.bcm.edu/lilab/liguow/RSeQC/figure/geneBody_coverage.png
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	51 :height: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	52 :width: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	53 :scale: 80 %
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	54
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	55 -----
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	56
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	57 About RSeQC
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	58 +++++++++++
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	59
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	60 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: 18 diff changeset	61
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	62 The RSeQC package is licensed under the GNU GPL v3 license.
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	63
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	64 .. image:: http://rseqc.sourceforge.net/_static/logo.png
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	65
cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	66 .. _RSeQC: http://rseqc.sourceforge.net/
18 64dc986da596 Uploaded nilesh parents: diff changeset	67
64dc986da596 Uploaded nilesh parents: diff changeset	68
64dc986da596 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>
31 cc5eaa9376d8 Lance's updates nilesh parents: 18 diff changeset	71 </tool>

Mercurial > repos > nilesh > rseqc

annotate geneBody_coverage2.xml @ 34:8fbd165f8835