annotate readdepth2sequencingdepth.xml @ 7:3c05abb4452e default tip

add missing files
author devteam@galaxyproject.org
date Wed, 22 Apr 2015 12:22:50 -0400
parents b27006b0a953
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
1 <tool id="readdepth2seqdepth" name="Convert informative read depth to sequencing depth" version="1.0.0">
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
2 <description>for flank-based mapping of microsatellites</description>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
3 <command interpreter="python2.7">sequencingdepthconversion_G.py $repeatlength $flanksize $readlength $infodepth $probprediction > $output </command>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
4
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
5 <inputs>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
6 <param name="repeatlength" type="integer" value="10" label="Repeat length (bp)" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
7 <param name="flanksize" type="integer" value="20" label="Required flank bases on each side in mapping" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
8 <param name="readlength" type="integer" value="100" label="Read length (treat all read as single end read)" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
9 <param name="infodepth" type="integer" value="5" label="Required read depth" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
10 <param name="probprediction" type="float" value="0.9" label="Proportion of genome that need certain level of read depth" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
11 </inputs>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
12 <outputs>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
13 <data format="input" name="output" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
14
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
15 </outputs>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
16 <tests>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
17 <!-- Test data with valid values -->
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
18 <test>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
19 <param name="repeatlength" value="10"/>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
20 <param name="flanksize" value="20" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
21 <param name="readlength" value="100" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
22 <param name="infodepth" value="5" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
23 <param name="probprediction" value="0.9" />
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
24 <output name="output" file="readdepth2seqdepth.out"/>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
25 </test>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
26
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
27 </tests>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
28 <help>
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
29
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
30
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
31 .. class:: infomark
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
32
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
33 **What it does**
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
34
5
b27006b0a953 update to latest version
devteam@galaxyproject.org
parents: 0
diff changeset
35 This tool is used to convert informative read depth (specified by user) to sequencing depth when the STRs is mapped using STR-FM pipeline.
b27006b0a953 update to latest version
devteam@galaxyproject.org
parents: 0
diff changeset
36 The locus specific sequencing depth (yrequired) is the sequencing depth that will make an STR locus to have a certain informative read depth based on uniform mapping of reads. It is calculated as follows: ::
0
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
37
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
38 yrequired = ( X * L ) / (L - (2F+r-1))
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
39
5
b27006b0a953 update to latest version
devteam@galaxyproject.org
parents: 0
diff changeset
40 where X = informative read depth, L = read length, F = the number of flanking bases required on either side, r = the expected repeat length of the STR of interest.
0
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
41
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
42 The genome wide sequencing depth is the sequencing depth that will make certain percentage of genome (e.g. 90 percent or 95 percent) to have certain locus specific sequencing depth. It's calculated using numerical guessing to find smallest lambda that: ::
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
43
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
44 0.90 (or other proportion specified by user) &lt; = P(Y=0) + P(Y=1) + …+ P(Y=yrequired-1)
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
45
5
b27006b0a953 update to latest version
devteam@galaxyproject.org
parents: 0
diff changeset
46 where P(Y=y) = (lambda^(y) * e ^(-lambda)) /y!
b27006b0a953 update to latest version
devteam@galaxyproject.org
parents: 0
diff changeset
47
0
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
48 y = specific level of sequencing depth. Lambda = genome wide sequencing depth
5
b27006b0a953 update to latest version
devteam@galaxyproject.org
parents: 0
diff changeset
49
b27006b0a953 update to latest version
devteam@galaxyproject.org
parents: 0
diff changeset
50 Please refer the Methods section of the paper cited below for further details.
0
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
51
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
52 **Citation**
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
53
5
b27006b0a953 update to latest version
devteam@galaxyproject.org
parents: 0
diff changeset
54 When you use this tool, please cite **Fungtammasan A, Ananda G, Hile SE, Su MS, Sun C, Harris R, Medvedev P, Eckert K, Makova KD. 2015. Accurate Typing of Short Tandem Repeats from Genome-wide Sequencing Data and its Applications, Genome Research**
0
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
55
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
56
20ab85af9505 Uploaded
arkarachai-fungtammasan
parents:
diff changeset
57 </help>
5
b27006b0a953 update to latest version
devteam@galaxyproject.org
parents: 0
diff changeset
58 </tool>