rseqc: clipping_profile.xml annotate

annotate clipping_profile.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_clipping_profile" name="Clipping Profile" 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 estimates clipping profile of RNA-seq reads from 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="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 clipping_profile.py -i $input -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: 16 diff changeset	13 <stdio>
cc5eaa9376d8 Lance's updates nilesh parents: 16 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: 16 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: 16 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 .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	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="xls" name="outputxls" from_work_dir="output.clipping_profile.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.clipping_profile.r" />
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 </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	24 <help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	25 clipping_profile.py
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	26 +++++++++++++++++++
16 366799f58c6b Uploaded nilesh parents: diff changeset	27
31 cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	28 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	29 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	30 (This means your reads aligner should support clipped mapping).
16 366799f58c6b Uploaded nilesh parents: diff changeset	31
366799f58c6b Uploaded nilesh parents: diff changeset	32 Inputs
366799f58c6b Uploaded nilesh parents: diff changeset	33 ++++++++++++++
366799f58c6b Uploaded nilesh parents: diff changeset	34
366799f58c6b Uploaded nilesh parents: diff changeset	35 Input BAM/SAM file
366799f58c6b Uploaded nilesh parents: diff changeset	36 Alignment file in BAM/SAM format.
366799f58c6b Uploaded nilesh parents: diff changeset	37
366799f58c6b Uploaded nilesh parents: diff changeset	38
366799f58c6b Uploaded nilesh parents: diff changeset	39 Sample Output
366799f58c6b Uploaded nilesh parents: diff changeset	40 ++++++++++++++
366799f58c6b Uploaded nilesh parents: diff changeset	41
31 cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	42 .. image:: http://rseqc.sourceforge.net/_images/clipping_good.png
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	43 :height: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	44 :width: 600 px
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	45 :scale: 80 %
31 cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	46
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	47 -----
16 366799f58c6b Uploaded nilesh parents: diff changeset	48
31 cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	49 About RSeQC
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	50 +++++++++++
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	51
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	52 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: 16 diff changeset	53
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	54 The RSeQC package is licensed under the GNU GPL v3 license.
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	55
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	56 .. image:: http://rseqc.sourceforge.net/_static/logo.png
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	57
cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	58 .. _RSeQC: http://rseqc.sourceforge.net/
16 366799f58c6b Uploaded nilesh parents: diff changeset	59
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 </help>
31 cc5eaa9376d8 Lance's updates nilesh parents: 16 diff changeset	61 </tool>

Mercurial > repos > nilesh > rseqc

annotate clipping_profile.xml @ 32:580ee0c4bc4e