Mercurial > repos > nilesh > rseqc

annotate read_quality.xml @ 49:6b33e31bda10 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
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 f242ee103277
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
1 <tool id="rseqc_read_quality" name="Read Quality" version="2.4galaxy1">
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
2 <description>determines Phred quality score</description>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
3
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
4 <macros>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
5 <import>rseqc_macros.xml</import>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
6 </macros>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
7
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
8 <requirements>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
9 <expand macro="requirement_package_r" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
10 <expand macro="requirement_package_numpy" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
11 <expand macro="requirement_package_rseqc" />
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
12 </requirements>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
13
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
14 <expand macro="stdio" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
15
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
16 <version_command><![CDATA[read_quality.py --version]]></version_command>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
17
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
18 <command><![CDATA[
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
19 read_quality.py
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
20 --input-file $input
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
21 --out-prefix output
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
22 -r $reduce
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
23 --mapq $mapq
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
24 ]]>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
25 </command>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
26
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
27 <inputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
28 <param name="input" type="data" format="bam,sam" label="input bam/sam file" help="(--input-file)"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
29 <param name="reduce" type="integer" label="Ignore Phred scores less than this amount (only applies to 'boxplot', default=1000)" value="1000" help="(--reduce)"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
30 <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" />
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
31 </inputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
32
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
33 <outputs>
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
34 <data format="txt" name="outputr" from_work_dir="output.qual.r" label="${tool.name} on ${on_string} (R Script)" />
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
35 <data format="pdf" name="outputheatpdf" from_work_dir="output.qual.heatmap.pdf" label="${tool.name} on ${on_string} (Heatmap PDF)" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
36 <data format="pdf" name="outputboxpdf" from_work_dir="output.qual.boxplot.pdf" label="${tool.name} on ${on_string} (Boxplot PDF)" />
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
37 </outputs>
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
38
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
39 <!-- Unable to succefully run this script with test data
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
40 <tests>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
41 <test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
42 <param name="input" value="pairend_strandspecific_51mer_hg19_chr1_1-100000.bigwig"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
43 <output name="outputr" file="output.qual.r"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
44 <output name="outputheatpdf" file="output.qual.heatmap.pdf"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
45 <output name="outputboxpdf" file="output.qual.boxplot.pdf"/>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
46 </test>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
47 </tests>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
48 -->
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
50 <help><![CDATA[
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
51 read_quality.py
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
52 +++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
53
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
54 According to SAM specification, if Q is the character to represent "base calling quality"
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
55 in SAM file, then Phred Quality Score = ord(Q) - 33. Here ord() is python function that
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
56 returns an integer representing the Unicode code point of the character when the argument
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
57 is a unicode object, for example, ord('a') returns 97. Phred quality score is widely used
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
58 to measure "reliability" of base-calling, for example, phred quality score of 20 means
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
59 there is 1/100 chance that the base-calling is wrong, phred quality score of 30 means there
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
60 is 1/1000 chance that the base-calling is wrong. In general: Phred quality score = -10xlog(10)P,
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
61 here P is probability that base-calling is wrong.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
62
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
63 Inputs
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
64 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
65
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
66 Input BAM/SAM file
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
67 Alignment file in BAM/SAM format.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
68
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
69 Ignore phred scores less than this number (default=1000)
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
70 To avoid making huge vector in R, nucleotide with certain phred score represented less than this number will be ignored. Increase this number save more memory while reduce precision. This option only applies to the 'boxplot'.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
71
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
72 Output
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
73 ++++++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
74
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
75 1. output.qual.r
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
76 2. output.qual.boxplot.pdf
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
77 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.plot.png
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
78 :height: 600 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
79 :width: 600 px
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
80 :scale: 80 %
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
81 3. output.qual.heatmap.pdf
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
82 .. image:: http://rseqc.sourceforge.net/_images/36mer.qual.heatmap.png
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
83 :height: 600 px
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
84 :width: 600 px
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
85 :scale: 80 %
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
86
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
87 Heatmap: use different color to represent nucleotide density ("blue"=low density,"orange"=median density,"red"=high density")
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
88
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
89 -----
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
90
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
91 About RSeQC
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
92 +++++++++++
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
93
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
94 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.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
95
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
96 The RSeQC package is licensed under the GNU GPL v3 license.
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
97
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
98 .. image:: http://rseqc.sourceforge.net/_static/logo.png
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
99
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
100 .. _RSeQC: http://rseqc.sourceforge.net/
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
101 ]]>
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
102 </help>
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
103
49
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
104 <expand macro="citations" />
6b33e31bda10 Uploaded tar based on https://github.com/lparsons/galaxy_tools/tree/master/tools/rseqc 1a3c419bc0ded7c40cb2bc3e7c87bfb01ddfeba2
lparsons
parents: 45
diff changeset
105
45
eb339c5849bb Reupload, toolshed removed all files of previous version.
lparsons
parents:
diff changeset
106 </tool>