rseqc: bam_stat.xml annotate

annotate bam_stat.xml @ 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

author	lparsons
date	Mon, 07 Oct 2013 15:01:13 -0400
parents	cc5eaa9376d8
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_bam_stat" name="BAM/SAM Mapping Stats" 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 reads mapping statistics for a provided BAM or 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	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="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	7 <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	8 </requirements>s
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 <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	10 bam_stat.py -i $input -q $mapqual 2> $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	11 </command>
31 cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	12 <stdio>
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	13 <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: 15 diff changeset	14 <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: 15 diff changeset	15 </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	16 <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	17 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" />
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 label="Minimum mapping quality (default=30" type="integer" value="30" name="mapqual" />
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 <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	21 <data format="txt" name="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	22 </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	23 <help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	24 bam_stat.py
15 2f55e1d520cd Uploaded nilesh parents: diff changeset	25 +++++++++++
2f55e1d520cd Uploaded nilesh parents: diff changeset	26
31 cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	27 This program is used to calculate reads mapping statistics from provided BAM
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	28 file. This script determines "uniquely mapped reads" from `mapping quality`_,
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	29 which quality the probability that a read is misplaced (Do NOT confused with
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	30 sequence quality, sequence quality measures the probability that a base-calling
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	31 was wrong) .
15 2f55e1d520cd Uploaded nilesh parents: diff changeset	32
2f55e1d520cd Uploaded nilesh parents: diff changeset	33 Inputs
2f55e1d520cd Uploaded nilesh parents: diff changeset	34 ++++++++++++++
2f55e1d520cd Uploaded nilesh parents: diff changeset	35
2f55e1d520cd Uploaded nilesh parents: diff changeset	36 Input BAM/SAM file
2f55e1d520cd Uploaded nilesh parents: diff changeset	37 Alignment file in BAM/SAM format.
2f55e1d520cd Uploaded nilesh parents: diff changeset	38
2f55e1d520cd Uploaded nilesh parents: diff changeset	39 Minimum mapping quality
2f55e1d520cd Uploaded nilesh parents: diff changeset	40 Minimum mapping quality for an alignment to be called “uniquely mapped” (default=30)
2f55e1d520cd Uploaded nilesh parents: diff changeset	41
2f55e1d520cd Uploaded nilesh parents: diff changeset	42 Output
2f55e1d520cd Uploaded nilesh parents: diff changeset	43 ++++++++++++++
2f55e1d520cd Uploaded nilesh parents: diff changeset	44
2f55e1d520cd Uploaded nilesh parents: diff changeset	45 - Total Reads (Total records) = {Multiple mapped reads} + {Uniquely mapped}
2f55e1d520cd Uploaded nilesh parents: diff changeset	46 - Uniquely mapped Reads = {read-1} + {read-2} (if paired end)
2f55e1d520cd Uploaded nilesh parents: diff changeset	47 - Uniquely mapped Reads = {Reads map to '+'} + {Reads map to '-'}
2f55e1d520cd Uploaded nilesh parents: diff changeset	48 - Uniquely mapped Reads = {Splice reads} + {Non-splice reads}
2f55e1d520cd Uploaded nilesh parents: diff changeset	49
31 cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	50 -----
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	51
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	52 About RSeQC
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	53 +++++++++++
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	54
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	55 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: 15 diff changeset	56
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	57 The RSeQC package is licensed under the GNU GPL v3 license.
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	58
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	59 .. image:: http://rseqc.sourceforge.net/_static/logo.png
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	60
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	61 .. _RSeQC: http://rseqc.sourceforge.net/
cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	62 .. _`mapping quality`: http://genome.sph.umich.edu/wiki/Mapping_Quality_Scores
15 2f55e1d520cd Uploaded nilesh parents: diff changeset	63
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	64 </help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 15 diff changeset	65 </tool>

Mercurial > repos > nilesh > rseqc

annotate bam_stat.xml @ 32:580ee0c4bc4e