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comparison read_duplication.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
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48:2e6190c29c54 49:6b33e31bda10
1 <tool id="rseqc_read_duplication" name="Read Duplication" version="2.4"> 1 <tool id="rseqc_read_duplication" name="Read Duplication" version="2.4galaxy1">
2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</description> 2 <description>determines reads duplication rate with sequence-based and mapping-based strategies</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
14 <expand macro="stdio" />
15
16 <version_command><![CDATA[read_duplication.py --version]]></version_command>
17
18 <command><![CDATA[
9 read_duplication.py -i $input -o output -u $upLimit 19 read_duplication.py -i $input -o output -u $upLimit
20 ]]>
10 </command> 21 </command>
11 <stdio> 22
12 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
13 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
14 </stdio>
15 <inputs> 23 <inputs>
16 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> 24 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
17 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" /> 25 <param name="upLimit" type="integer" label="Upper Limit of Plotted Duplicated Times (default=500)" value="500" help="(--up-limit)"/>
18 </inputs> 26 </inputs>
27
19 <outputs> 28 <outputs>
20 <data format="xls" name="outputxls" from_work_dir="output.dup.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/> 29 <data format="xls" name="outputxls" from_work_dir="output.pos.DupRate.xls" label="${tool.name} on ${on_string} (Position XLS)"/>
21 <data format="xls" name="outputseqxls" from_work_dir="output.dup.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/> 30 <data format="xls" name="outputseqxls" from_work_dir="output.seq.DupRate.xls" label="${tool.name} on ${on_string} (Sequence XLS)"/>
22 <data format="txt" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" /> 31 <data format="txt" name="outputr" from_work_dir="output.DupRate_plot.r" label="${tool.name} on ${on_string} (R Script)" />
23 <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" /> 32 <data format="pdf" name="outputpdf" from_work_dir="output.DupRate_plot.pdf" label="${tool.name} on ${on_string} (PDF)" />
24 </outputs> 33 </outputs>
25 <help> 34
35 <tests>
36 <test>
37 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
38 <output name="outputxls" file="output.pos.DupRate.xls"/>
39 <output name="outputseqxls" file="output.seq.DupRate.xls"/>
40 <output name="outputr" file="output.DupRate_plot.r"/>
41 </test>
42 </tests>
43
44 <help><![CDATA[
26 read_duplication.py 45 read_duplication.py
27 +++++++++++++++++++ 46 +++++++++++++++++++
28 47
29 Two strategies were used to determine reads duplication rate: 48 Two strategies were used to determine reads duplication rate:
30 49
31 * Sequence based: reads with exactly the same sequence content are regarded as duplicated reads. 50 * Sequence based: reads with exactly the same sequence content are regarded as duplicated reads.
32 * Mapping based: reads mapped to the same genomic location are regarded as duplicated reads. For splice reads, reads mapped to the same starting position and splice the same way are regarded as duplicated reads. 51 * Mapping based: reads mapped to the same genomic location are regarded as duplicated reads. For splice reads, reads mapped to the same starting position and splice the same way are regarded as duplicated reads.
33 52
34 Inputs 53 Inputs
35 ++++++++++++++ 54 ++++++++++++++
36 55
37 Input BAM/SAM file 56 Input BAM/SAM file
49 4. output.DupRate_plot.pdf: graphical output generated from R script 68 4. output.DupRate_plot.pdf: graphical output generated from R script
50 69
51 .. image:: http://rseqc.sourceforge.net/_images/duplicate.png 70 .. image:: http://rseqc.sourceforge.net/_images/duplicate.png
52 :height: 600 px 71 :height: 600 px
53 :width: 600 px 72 :width: 600 px
54 :scale: 80 % 73 :scale: 80 %
55 74
56 ----- 75 -----
57 76
58 About RSeQC 77 About RSeQC
59 +++++++++++ 78 +++++++++++
60 79
61 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. 80 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.
62 81
63 The RSeQC package is licensed under the GNU GPL v3 license. 82 The RSeQC package is licensed under the GNU GPL v3 license.
64 83
65 .. image:: http://rseqc.sourceforge.net/_static/logo.png 84 .. image:: http://rseqc.sourceforge.net/_static/logo.png
66 85
67 .. _RSeQC: http://rseqc.sourceforge.net/ 86 .. _RSeQC: http://rseqc.sourceforge.net/
87 ]]>
88 </help>
68 89
90 <expand macro="citations" />
69 91
70 </help>
71 </tool> 92 </tool>