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comparison clipping_profile.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_clipping_profile" name="Clipping Profile" version="2.4"> 1 <tool id="rseqc_clipping_profile" name="Clipping Profile" version="2.4galaxy1">
2 <description> 2 <description>
3 estimates clipping profile of RNA-seq reads from BAM or SAM file 3 estimates clipping profile of RNA-seq reads from BAM or SAM file
4 </description> 4 </description>
5
6 <macros>
7 <import>rseqc_macros.xml</import>
8 </macros>
9
5 <requirements> 10 <requirements>
6 <requirement type="package" version="3.0.3">R</requirement> 11 <expand macro="requirement_package_r" />
7 <requirement type="package" version="1.7.1">numpy</requirement> 12 <expand macro="requirement_package_numpy" />
8 <requirement type="package" version="2.4">rseqc</requirement> 13 <expand macro="requirement_package_rseqc" />
9 </requirements> 14 </requirements>
10 <command> 15
16 <expand macro="stdio" />
17
18 <version_command><![CDATA[clipping_profile.py --version]]></version_command>
19
20 <command><![CDATA[
11 clipping_profile.py -i $input -o output 21 clipping_profile.py -i $input -o output
22 ]]>
12 </command> 23 </command>
13 <stdio> 24
14 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
15 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
16 </stdio>
17 <inputs> 25 <inputs>
18 <param name="input" type="data" label="Input .bam/.sam File" format="bam,sam" /> 26 <param name="input" type="data" label="Input .bam File" format="bam" help="(--input-file)"/>
19 </inputs> 27 </inputs>
28
20 <outputs> 29 <outputs>
30 <data format="pdf" name="outputpdf" from_work_dir="output.clipping_profile.pdf" />
21 <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" /> 31 <data format="xls" name="outputxls" from_work_dir="output.clipping_profile.xls" />
22 <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" /> 32 <data format="txt" name="outputr" from_work_dir="output.clipping_profile.r" />
23 </outputs> 33 </outputs>
24 <help> 34
35 <tests>
36 <test>
37 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
38 <output name="outputpdf" file="output.clipping_profile.pdf"/>
39 <output name="outputxls" file="output.clipping_profile.xls"/>
40 <output name="outputr" file="output.clipping_profile.r"/>
41 </test>
42 </tests>
43
44 <help><![CDATA[
25 clipping_profile.py 45 clipping_profile.py
26 +++++++++++++++++++ 46 +++++++++++++++++++
27 47
28 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file. 48 This program is used to estimate clipping profile of RNA-seq reads from BAM or SAM file.
29 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation 49 Note that to use this funciton, CIGAR strings within SAM/BAM file should have 'S' operation
44 :width: 600 px 64 :width: 600 px
45 :scale: 80 % 65 :scale: 80 %
46 66
47 ----- 67 -----
48 68
49 About RSeQC 69 About RSeQC
50 +++++++++++ 70 +++++++++++
51 71
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. 72 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.
53 73
54 The RSeQC package is licensed under the GNU GPL v3 license. 74 The RSeQC package is licensed under the GNU GPL v3 license.
55 75
56 .. image:: http://rseqc.sourceforge.net/_static/logo.png 76 .. image:: http://rseqc.sourceforge.net/_static/logo.png
57 77
58 .. _RSeQC: http://rseqc.sourceforge.net/ 78 .. _RSeQC: http://rseqc.sourceforge.net/
79 ]]>
80 </help>
59 81
60 </help> 82 <expand macro="citations" />
83
61 </tool> 84 </tool>