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comparison tools/rgenetics/rgEigPCA.xml @ 0:9071e359b9a3

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date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="rgEigPCA1" name="Eigensoft:">
2 <description>PCA Ancestry using SNP</description>
3
4 <command interpreter="python">
5 rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1"
6 "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca"
7 </command>
8
9 <inputs>
10
11 <param name="i" type="data" label="Input genotype data file"
12 size="120" format="ldindep" />
13 <param name="title" type="text" value="Ancestry PCA" label="Title for outputs from this run"
14 size="80" />
15 <param name="k" type="integer" value="4" label="Number of principal components to output"
16 size="3" />
17 <param name="m" type="integer" value="0" label="Max. outlier removal iterations"
18 help="To turn on outlier removal, set m=5 or so. Do this if you plan on adjusting any analyses"
19 size="3" />
20 <param name="t" type="integer" value="5" label="# principal components used for outlier removal"
21 size="3" />
22 <param name="s" type="integer" value="6" label="#SDs for outlier removal"
23 help = "Any individual with SD along one of k top principal components > s will be removed as an outlier."
24 size="3" />
25
26 </inputs>
27
28 <outputs>
29 <data name="out_file1" format="html" label="${title}_rgEig.html"/>
30 <data name="pca" format="txt" label="${title}_rgEig.txt"/>
31 </outputs>
32
33 <tests>
34 <test>
35 <param name='i' value='tinywga' ftype='ldindep' >
36 <metadata name='base_name' value='tinywga' />
37 <composite_data value='tinywga.bim' />
38 <composite_data value='tinywga.bed' />
39 <composite_data value='tinywga.fam' />
40 <edit_attributes type='name' value='tinywga' />
41 </param>
42 <param name='title' value='rgEigPCAtest1' />
43 <param name="k" value="4" />
44 <param name="m" value="2" />
45 <param name="t" value="2" />
46 <param name="s" value="2" />
47 <output name='out_file1' file='rgtestouts/rgEigPCA/rgEigPCAtest1.html' ftype='html' compare='diff' lines_diff='195'>
48 <extra_files type="file" name='rgEigPCAtest1_PCAPlot.pdf' value="rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf" compare="sim_size" delta="3000"/>
49 </output>
50 <output name='pca' file='rgtestouts/rgEigPCA/rgEigPCAtest1.txt' compare='diff'/>
51 </test>
52 </tests>
53
54 <help>
55
56
57 **Syntax**
58
59 - **Genotype data** is an input genotype dataset in Plink lped (http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml) format. See below for notes
60 - **Title** is used to name the output files so you can remember what the outputs are for
61 - **Tuning parameters** are documented in the Eigensoft (http://genepath.med.harvard.edu/~reich/Software.htm) documentation - see below
62
63
64 -----
65
66 **Summary**
67
68 Eigensoft requires ld-reduced genotype data.
69 Galaxy has an automatic converter for genotype data in Plink linkage pedigree (lped) format.
70 For details of this generic genotype format, please see the Plink documentation at
71 http://pngu.mgh.harvard.edu/~purcell/plink/data.shtml
72
73 Reading that documentation, you'll see that the linkage pedigree format is really two related files with the same
74 file base name - a map and ped file - eg 'mygeno.ped' and 'mygeno.map'.
75 The map file has the chromosome, offset, genetic offset and snp name corresponding to each
76 genotype stored as separate alleles in the ped file. The ped file has family id, individual id, father id (or 0), mother id
77 (or 0), gender (1=male, 2=female, 0=unknown) and affection (1=unaffected, 2=affected, 0=unknown),
78 then two separate allele columns for each genotype.
79
80 Once you have your data in the right format, you can upload those into your Galaxy history using the "upload" tool.
81
82 To upload your lped data in the upload tool, choose 'lped' as the 'file format'. The tool form will change to
83 allow you to navigate to and select each member of the pair of ped and map files stored on your local computer
84 (or available at a public URL for Galaxy to grab).
85 Give the dataset a meaningful name (replace rgeneticsData with something more useful!) and click execute.
86
87 When the upload is done, your new lped format dataset will appear in your history and then,
88 when you choose the ancestry tool, that history dataset will be available as input.
89
90 **Warning for the Impatient**
91
92 When you execute the tool, it will look like it has not started running for a while as the automatic converter
93 reduces the amount of LD - otherwise eigenstrat gives biased results.
94
95
96 **Attribution**
97
98 This tool runs and relies on the work of many others, including the
99 maintainers of the Eigensoft program, and the R and
100 Bioconductor projects. For full attribution, source code and documentation, please see
101 http://genepath.med.harvard.edu/~reich/Software.htm, http://cran.r-project.org/
102 and http://www.bioconductor.org/ respectively
103
104 This implementation is a Galaxy tool wrapper around these third party applications.
105 It was originally designed and written for family based data from the CAMP Illumina run of 2007 by
106 ross lazarus (ross.lazarus@gmail.com) and incorporated into the rgenetics toolkit.
107
108 copyright Ross Lazarus 2007
109 Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html
110 but is about as useful as a sponge boat without EIGENSOFT pca code.
111
112 **README from eigensoft2 distribution at http://genepath.med.harvard.edu/~reich/Software.htm**
113
114 [rerla@beast eigensoft2]$ cat README
115 EIGENSOFT version 2.0, January 2008 (for Linux only)
116
117 This is the same as our EIGENSOFT 2.0 BETA release with a few recent changes
118 as described at http://genepath.med.harvard.edu/~reich/New_In_EIGENSOFT.htm.
119
120 Features of EIGENSOFT version 2.0 include:
121 -- Keeping track of ref/var alleles in all file formats: see CONVERTF/README
122 -- Handling data sets up to 8 billion genotypes: see CONVERTF/README
123 -- Output SNP weightings of each principal component: see POPGEN/README
124
125 The EIGENSOFT package implements methods from the following 2 papers:
126 Patterson N. et al. 2006 PLoS Genetics in press (population structure)
127 Price A.L. et al. 2006 NG 38:904-9 (EIGENSTRAT stratification correction)
128
129 See POPGEN/README for documentation of population structure programs.
130
131 See EIGENSTRAT/README for documentation of EIGENSTRAT programs.
132
133 See CONVERTF/README for documentation of programs for converting file formats.
134
135
136 Executables and source code:
137 ----------------------------
138 All C executables are in the bin/ directory.
139
140 We have placed source code for all C executables in the src/ directory,
141 for users who wish to modify and recompile our programs. For example, to
142 recompile the eigenstrat program, type
143 "cd src"
144 "make eigenstrat"
145 "mv eigenstrat ../bin"
146
147 Note that some of our software will only compile if your system has the
148 lapack package installed. (This package is used to compute eigenvectors.)
149 Some users may need to change "blas-3" to "blas" in the Makefile,
150 depending on how blas and lapack are installed.
151
152 If cc is not available on your system, try "cp Makefile.alt Makefile"
153 and then recompile.
154
155 If you have trouble compiling and running our code, try compiling and
156 running the pcatoy program in the src directory:
157 "cd src"
158 "make pcatoy"
159 "./pcatoy"
160 If you are unable to run the pcatoy program successfully, please contact
161 your system administrator for help, as this is a systems issue which is
162 beyond our scope. Your system administrator will be able to troubleshoot
163 your systems issue using this trivial program. [You can also try running
164 the pcatoy program in the bin directory, which we have already compiled.]
165 </help>
166 </tool>
167