root/galaxy-central/tools/rgenetics/rgEigPCA.xml

リビジョン 2, 5.6 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

行番号 
1<tool id="rgEigPCA1" name="Eigensoft:">
2    <code file="rgEigPCA_code.py"/>
3    <description>PCA Ancestry using SNP</description>
4
5    <command interpreter="python">
6    rgEigPCA.py "$i.extra_files_path/$i.metadata.base_name" "$title" "$out_file1"
7    "$out_file1.files_path" "$k" "$m" "$t" "$s" "$pca"
8    </command>
9
10    <inputs>
11
12       <param name="i"  type="data" label="Input genotype data file"
13          size="120" format="ldindep" />
14       <param name="title"  type="text" value="Ancestry PCA" label="Title for outputs from this run"
15          size="80"  />
16       <param name="k"  type="integer" value="4" label="Number of principal components to output"
17          size="3"  />
18       <param name="m"  type="integer" value="0" label="Max. outlier removal iterations"
19          help="To turn on outlier removal, set m=5 or so. Do this if you plan on adjusting any analyses"
20          size="3"  />
21       <param name="t"  type="integer" value="5" label="# principal components used for outlier removal"
22          size="3"  />
23       <param name="s"  type="integer" value="6" label="#SDs for outlier removal"
24          help = "Any individual with SD along one of k top principal components > s will be removed as an outlier."
25          size="3"  />
26
27   </inputs>
28
29   <outputs>
30       <data name="out_file1" format="html" />
31       <data name="pca" format="txt" />
32   </outputs>
33
34<!-- python $TOOLPATH/$TOOL.py "$INPATH/tinywga" "$NPRE" ${OUTPATH}/${NPRE}.html $OUTPATH 4 2 2 2 $OUTPATH/pca.out $BINPATH -->
35
36<tests>
37 <test>
38   <param name='i' value='tinywga' ftype='ldindep' >
39   <metadata name='base_name' value='tinywga' />
40   <composite_data value='tinywga.bim' />
41   <composite_data value='tinywga.bed' />
42   <composite_data value='tinywga.fam' />
43   <edit_attributes type='name' value='tinywga' />
44   </param>
45    <param name='title' value='rgEigPCAtest1' />
46    <param name="k" value="4" />
47    <param name="m" value="2" />
48    <param name="t" value="2" />
49    <param name="s" value="2" />
50    <output name='out_file1' file='rgtestouts/rgEigPCA/rgEigPCAtest1.html' ftype='html' compare='diff' lines_diff='195'>
51    <extra_files type="file" name='rgEigPCAtest1_PCAPlot.pdf' value="rgtestouts/rgEigPCA/rgEigPCAtest1_PCAPlot.pdf" compare="sim_size" delta="3000"/>
52    </output>
53    <output name='pca' file='rgtestouts/rgEigPCA/rgEigPCAtest1.txt' compare='diff'/>
54 </test>
55</tests>
56
57<help>
58
59
60**Syntax**
61
62- **Genotype data** is the input genotype file chosen from available library files.
63- **Title** is used to name the output files
64- **Tuning parameters** documented in the Eigensoft documentation - see below
65
66(Note that you may need to convert an existing genotype file into that format to use this tool)
67
68-----
69
70**Summary**
71
72**Attribution**
73This tool runs and relies on the work of many others, including the
74maintainers of the Eigensoft program, and the R and
75Bioconductor projects. For full attribution, source code and documentation, please see
76http://genepath.med.harvard.edu/~reich/Software.htm, http://cran.r-project.org/
77and http://www.bioconductor.org/ respectively
78
79This implementation is a Galaxy tool wrapper around these third party applications.
80It was originally designed and written for family based data from the CAMP Illumina run of 2007 by
81ross lazarus (ross.lazarus@gmail.com) and incorporated into the rgenetics toolkit.
82
83copyright Ross Lazarus 2007
84Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html
85but is about as useful as a sponge boat without EIGENSOFT pca code.
86
87**README from eigensoft2**
88
89[rerla@beast eigensoft2]$ cat README
90EIGENSOFT version 2.0, January 2008 (for Linux only)
91
92This is the same as our EIGENSOFT 2.0 BETA release with a few recent changes
93as described at http://genepath.med.harvard.edu/~reich/New_In_EIGENSOFT.htm.
94
95Features of EIGENSOFT version 2.0 include:
96-- Keeping track of ref/var alleles in all file formats: see CONVERTF/README
97-- Handling data sets up to 8 billion genotypes: see CONVERTF/README
98-- Output SNP weightings of each principal component: see POPGEN/README
99
100The EIGENSOFT package implements methods from the following 2 papers:
101Patterson N. et al. 2006 PLoS Genetics in press (population structure)
102Price A.L. et al. 2006 NG 38:904-9 (EIGENSTRAT stratification correction)
103
104See POPGEN/README for documentation of population structure programs.
105
106See EIGENSTRAT/README for documentation of EIGENSTRAT programs.
107
108See CONVERTF/README for documentation of programs for converting file formats.
109
110
111Executables and source code:
112----------------------------
113All C executables are in the bin/ directory.
114
115We have placed source code for all C executables in the src/ directory,
116for users who wish to modify and recompile our programs.  For example, to
117recompile the eigenstrat program, type
118"cd src"
119"make eigenstrat"
120"mv eigenstrat ../bin"
121
122Note that some of our software will only compile if your system has the
123lapack package installed.  (This package is used to compute eigenvectors.)
124Some users may need to change "blas-3" to "blas" in the Makefile,
125depending on how blas and lapack are installed.
126
127If cc is not available on your system, try "cp Makefile.alt Makefile"
128and then recompile.
129
130If you have trouble compiling and running our code, try compiling and
131running the pcatoy program in the src directory:
132"cd src"
133"make pcatoy"
134"./pcatoy"
135If you are unable to run the pcatoy program successfully, please contact
136your system administrator for help, as this is a systems issue which is
137beyond our scope.  Your system administrator will be able to troubleshoot
138your systems issue using this trivial program.  [You can also try running
139the pcatoy program in the bin directory, which we have already compiled.]
140</help>
141</tool>
142
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