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comparison read_distribution.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_distribution" name="Read Distribution" version="2.4"> 1 <tool id="rseqc_read_distribution" name="Read Distribution" version="2.4galaxy1">
2 <description>calculates how mapped reads were distributed over genome feature</description> 2 <description>calculates how mapped reads were distributed over genome feature</description>
3
4 <macros>
5 <import>rseqc_macros.xml</import>
6 </macros>
7
3 <requirements> 8 <requirements>
4 <requirement type="package" version="1.7.1">numpy</requirement> 9 <expand macro="requirement_package_numpy" />
5 <requirement type="package" version="2.4">rseqc</requirement> 10 <expand macro="requirement_package_rseqc" />
6 </requirements> 11 </requirements>
7 <command> 12
13 <expand macro="stdio" />
14
15 <version_command><![CDATA[read_distribution.py --version]]></version_command>
16
17 <command><![CDATA[
8 read_distribution.py -i $input -r $refgene > $output 18 read_distribution.py -i $input -r $refgene > $output
19 ]]>
9 </command> 20 </command>
10 <stdio> 21
11 <exit_code range="1:" level="fatal" description="An error occured during execution, see stderr and stdout for more information" />
12 <regex match="[Ee]rror" source="both" description="An error occured during execution, see stderr and stdout for more information" />
13 </stdio>
14 <inputs> 22 <inputs>
15 <param name="input" type="data" format="bam,sam" label="input bam/sam file" /> 23 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
16 <param name="refgene" type="data" format="bed" label="reference gene model" /> 24 <param name="refgene" type="data" format="bed" label="reference gene model" help="(--refgene)"/>
17 </inputs> 25 </inputs>
26
18 <outputs> 27 <outputs>
19 <data format="txt" name="output" /> 28 <data format="txt" name="output" />
20 </outputs> 29 </outputs>
21 <help> 30
31 <tests>
32 <test>
33 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bam"/>
34 <param name="refgene" value="hg19_RefSeq_chr1_1-100000.bed"/>
35 <output name="output" file="output.read_distribution.txt"/>
36 </test>
37 </tests>
38
39 <help><![CDATA[
22 read_distribution.py 40 read_distribution.py
23 ++++++++++++++++++++ 41 ++++++++++++++++++++
24 42
25 Provided a BAM/SAM file and reference gene model, this module will calculate how mapped 43 Provided a BAM/SAM file and reference gene model, this module will calculate how mapped
26 reads were distributed over genome feature (like CDS exon, 5'UTR exon, 3' UTR exon, Intron, 44 reads were distributed over genome feature (like CDS exon, 5'UTR exon, 3' UTR exon, Intron,
37 55
38 RSeQC cannot assign those reads that: 56 RSeQC cannot assign those reads that:
39 57
40 * hit to intergenic regions that beyond region starting from TSS upstream 10Kb to TES downstream 10Kb. 58 * hit to intergenic regions that beyond region starting from TSS upstream 10Kb to TES downstream 10Kb.
41 * hit to regions covered by both 5'UTR and 3' UTR. This is possible when two head-to-tail transcripts are overlapped in UTR regions. 59 * hit to regions covered by both 5'UTR and 3' UTR. This is possible when two head-to-tail transcripts are overlapped in UTR regions.
42 * hit to regions covered by both TSS upstream 10Kb and TES downstream 10Kb. 60 * hit to regions covered by both TSS upstream 10Kb and TES downstream 10Kb.
43 61
44 62
45 Inputs 63 Inputs
46 ++++++++++++++ 64 ++++++++++++++
47 65
55 ++++++++++++++ 73 ++++++++++++++
56 74
57 Output: 75 Output:
58 76
59 =============== ============ =========== =========== 77 =============== ============ =========== ===========
60 Group Total_bases Tag_count Tags/Kb 78 Group Total_bases Tag_count Tags/Kb
61 =============== ============ =========== =========== 79 =============== ============ =========== ===========
62 CDS_Exons 33302033 20002271 600.63 80 CDS_Exons 33302033 20002271 600.63
63 5'UTR_Exons 21717577 4408991 203.01 81 5'UTR_Exons 21717577 4408991 203.01
64 3'UTR_Exons 15347845 3643326 237.38 82 3'UTR_Exons 15347845 3643326 237.38
65 Introns 1132597354 6325392 5.58 83 Introns 1132597354 6325392 5.58
66 TSS_up_1kb 17957047 215331 11.99 84 TSS_up_1kb 17957047 215331 11.99
67 TSS_up_5kb 81621382 392296 4.81 85 TSS_up_5kb 81621382 392296 4.81
68 TSS_up_10kb 149730983 769231 5.14 86 TSS_up_10kb 149730983 769231 5.14
69 TES_down_1kb 18298543 266161 14.55 87 TES_down_1kb 18298543 266161 14.55
70 TES_down_5kb 78900674 729997 9.25 88 TES_down_5kb 78900674 729997 9.25
71 TES_down_10kb 140361190 896882 6.39 89 TES_down_10kb 140361190 896882 6.39
72 =============== ============ =========== =========== 90 =============== ============ =========== ===========
73 91
74 ----- 92 -----
75 93
76 About RSeQC 94 About RSeQC
77 +++++++++++ 95 +++++++++++
78 96
79 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. 97 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 98
81 The RSeQC package is licensed under the GNU GPL v3 license. 99 The RSeQC package is licensed under the GNU GPL v3 license.
82 100
83 .. image:: http://rseqc.sourceforge.net/_static/logo.png 101 .. image:: http://rseqc.sourceforge.net/_static/logo.png
84 102
85 .. _RSeQC: http://rseqc.sourceforge.net/ 103 .. _RSeQC: http://rseqc.sourceforge.net/
104 ]]>
105 </help>
86 106
107 <expand macro="citations" />
87 108
88
89 </help>
90 </tool> 109 </tool>