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comparison read_GC.xml @ 40:1e66f05a23aa

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Reupload tarball (all files were again deleted by toolshed).
author lparsons
date Wed, 23 Jul 2014 10:44:50 -0400
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39:1b769e35cd8e 40:1e66f05a23aa
1 <tool id="rseqc_read_GC" name="Read GC" version="2.3.9">
2 <description>determines GC% and read count</description>
3 <requirements>
4 <requirement type="package" version="3.0.1">R</requirement>
5 <requirement type="package" version="1.7.1">numpy</requirement>
6 <requirement type="package" version="2.3.9">rseqc</requirement>
7 </requirements>
8 <command>
9 read_GC.py -i $input -o output
10 </command>
11 <stdio>
12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
14 </stdio>
15 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" />
17 </inputs>
18 <outputs>
19 <data format="xls" name="outputxls" from_work_dir="output.GC.xls" label="${tool.name} on ${on_string} (XLS)"/>
20 <data format="txt" name="outputr" from_work_dir="output.GC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
21 <data format="pdf" name="outputpdf" from_work_dir="output.GC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
22 </outputs>
23 <help>
24 read_GC.py
25 ++++++++++
26
27
28 Inputs
29 ++++++++++++++
30
31 Input BAM/SAM file
32 Alignment file in BAM/SAM format.
33
34 Output
35 ++++++++++++++
36
37 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count
38 2. output.GC_plot.r: R script to generate pdf file.
39 3. output.GC_plot.pdf: graphical output generated from R script.
40
41 .. image:: http://rseqc.sourceforge.net/_images/read_gc.png
42 :height: 600 px
43 :width: 600 px
44 :scale: 80 %
45
46 -----
47
48 About RSeQC
49 +++++++++++
50
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.
52
53 The RSeQC package is licensed under the GNU GPL v3 license.
54
55 .. image:: http://rseqc.sourceforge.net/_static/logo.png
56
57 .. _RSeQC: http://rseqc.sourceforge.net/
58
59
60 </help>
61 </tool>