rseqc: read_GC.xml annotate

annotate read_GC.xml @ 35:ff21a055413b

Create lib directories during install, added README.txt

author	lparsons
date	Tue, 22 Jul 2014 16:52:10 -0400
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_GC" name="Read GC" 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 GC% and read count</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_GC.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	10 </command>
31 cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	11 <stdio>
cc5eaa9376d8 Lance's updates nilesh parents: 25 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: 25 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: 25 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 </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 <outputs>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	19 <data format="xls" name="outputxls" from_work_dir="output.GC.xls" label="${tool.name} on ${on_string} (XLS)"/>
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	20 <data format="txt" name="outputr" from_work_dir="output.GC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
580ee0c4bc4e Fixes from Bjorn Gruning: create symlinks under $TMP and clean them up afterwards, replace R dependency with the Tool Shed R3 package, add --install-scripts, prepend tool-ids with rseqc lparsons parents: 31 diff changeset	21 <data format="pdf" name="outputpdf" from_work_dir="output.GC_plot.pdf" label="${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	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: 25 diff changeset	24 read_GC.py
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	25 ++++++++++
25 7cac660d1c0a Uploaded nilesh parents: diff changeset	26
7cac660d1c0a Uploaded nilesh parents: diff changeset	27
7cac660d1c0a Uploaded nilesh parents: diff changeset	28 Inputs
7cac660d1c0a Uploaded nilesh parents: diff changeset	29 ++++++++++++++
7cac660d1c0a Uploaded nilesh parents: diff changeset	30
7cac660d1c0a Uploaded nilesh parents: diff changeset	31 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	32 Alignment file in BAM/SAM format.
25 7cac660d1c0a Uploaded nilesh parents: diff changeset	33
7cac660d1c0a Uploaded nilesh parents: diff changeset	34 Output
7cac660d1c0a Uploaded nilesh parents: diff changeset	35 ++++++++++++++
7cac660d1c0a Uploaded nilesh parents: diff changeset	36
7cac660d1c0a Uploaded nilesh parents: diff changeset	37 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count
7cac660d1c0a Uploaded nilesh parents: diff changeset	38 2. output.GC_plot.r: R script to generate pdf file.
7cac660d1c0a Uploaded nilesh parents: diff changeset	39 3. output.GC_plot.pdf: graphical output generated from R script.
7cac660d1c0a Uploaded nilesh parents: diff changeset	40
31 cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	41 .. image:: http://rseqc.sourceforge.net/_images/read_gc.png
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	42 :height: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	43 :width: 600 px
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	44 :scale: 80 %
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	45
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	46 -----
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	47
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	48 About RSeQC
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	49 +++++++++++
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	50
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	51 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: 25 diff changeset	52
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	53 The RSeQC package is licensed under the GNU GPL v3 license.
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	54
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	55 .. image:: http://rseqc.sourceforge.net/_static/logo.png
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	56
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	57 .. _RSeQC: http://rseqc.sourceforge.net/
cc5eaa9376d8 Lance's updates nilesh parents: 25 diff changeset	58
25 7cac660d1c0a 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>
25 7cac660d1c0a Uploaded nilesh parents: diff changeset	61 </tool>

Mercurial > repos > nilesh > rseqc

annotate read_GC.xml @ 35:ff21a055413b