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comparison read_GC.xml @ 49:6b33e31bda10 draft

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Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
author lparsons
date Thu, 16 Jul 2015 17:43:43 -0400
parents eb339c5849bb
children 09846d5169fa
comparison
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48:2e6190c29c54 49:6b33e31bda10
1 <tool id="rseqc_read_GC" name="Read GC" version="2.4"> 1 <tool id="rseqc_read_GC" name="Read GC" version="2.4galaxy1">
2 <description>determines GC% and read count</description> 2 <description>determines GC% and read count</description>
3
4 <macros>
5 <import>rseqc_macros.xml</import>
6 </macros>
7
3 <requirements> 8 <requirements>
4 <requirement type="package" version="3.0.3">R</requirement> 9 <expand macro="requirement_package_r" />
5 <requirement type="package" version="1.7.1">numpy</requirement> 10 <expand macro="requirement_package_numpy" />
6 <requirement type="package" version="2.4">rseqc</requirement> 11 <expand macro="requirement_package_rseqc" />
7 </requirements> 12 </requirements>
8 <command> 13
9 read_GC.py -i $input -o output 14 <expand macro="stdio" />
15
16 <version_command><![CDATA[read_GC.py --version]]></version_command>
17
18 <command><![CDATA[
19 read_GC.py
20 --input-file $input
21 --out-prefix output
22 --mapq $mapq
23 ]]>
10 </command> 24 </command>
11 <stdio> 25
12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
14 </stdio>
15 <inputs> 26 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> 27 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
28 <param name="mapq" type="integer" label="Minimum mapping quality (default=30)" help="Minimum phred scale mapping quality to consider a read 'uniquely mapped' (--mapq)" value="30" />
17 </inputs> 29 </inputs>
30
18 <outputs> 31 <outputs>
19 <data format="xls" name="outputxls" from_work_dir="output.GC.xls" label="${tool.name} on ${on_string} (XLS)"/> 32 <data format="xls" name="outputxls" from_work_dir="output.GC.xls" label="${tool.name} on ${on_string} (XLS)"/>
20 <data format="txt" name="outputr" from_work_dir="output.GC_plot.r" label="${tool.name} on ${on_string} (R Script)" /> 33 <data format="txt" name="outputr" from_work_dir="output.GC_plot.r" label="${tool.name} on ${on_string} (R Script)" />
21 <data format="pdf" name="outputpdf" from_work_dir="output.GC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> 34 <data format="pdf" name="outputpdf" from_work_dir="output.GC_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
22 </outputs> 35 </outputs>
23 <help> 36
37 <tests>
38 <test>
39 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
40 <output name="outputxls" file="output.GC.xls"/>
41 <output name="outputr" file="output.GC_plot.r"/>
42 </test>
43 </tests>
44
45 <help><![CDATA[
24 read_GC.py 46 read_GC.py
25 ++++++++++ 47 ++++++++++
26 48
27 49
28 Inputs 50 Inputs
34 Output 56 Output
35 ++++++++++++++ 57 ++++++++++++++
36 58
37 1. output.GC.xls: Two column, plain text file, first column is GC%, second column is read count 59 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. 60 2. output.GC_plot.r: R script to generate pdf file.
39 3. output.GC_plot.pdf: graphical output generated from R script. 61 3. output.GC_plot.pdf: graphical output generated from R script.
40 62
41 .. image:: http://rseqc.sourceforge.net/_images/read_gc.png 63 .. image:: http://rseqc.sourceforge.net/_images/read_gc.png
42 :height: 600 px 64 :height: 600 px
43 :width: 600 px 65 :width: 600 px
44 :scale: 80 % 66 :scale: 80 %
45 67
46 ----- 68 -----
47 69
48 About RSeQC 70 About RSeQC
49 +++++++++++ 71 +++++++++++
50 72
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. 73 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 74
53 The RSeQC package is licensed under the GNU GPL v3 license. 75 The RSeQC package is licensed under the GNU GPL v3 license.
54 76
55 .. image:: http://rseqc.sourceforge.net/_static/logo.png 77 .. image:: http://rseqc.sourceforge.net/_static/logo.png
56 78
57 .. _RSeQC: http://rseqc.sourceforge.net/ 79 .. _RSeQC: http://rseqc.sourceforge.net/
80 ]]>
81 </help>
58 82
83 <expand macro="citations" />
59 84
60 </help>
61 </tool> 85 </tool>