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

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author xuebing
date Fri, 09 Mar 2012 19:37:19 -0500
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1 <tool id="rgTDT1" name="Transmission Distortion:">
2 <description>for family data</description>
3
4 <command interpreter="python">
5 rgTDT.py -i '$i.extra_files_path/$i.metadata.base_name' -o '$title'
6 -r '$out_file1' -l '$logf' -g '$gffout'
7 </command>
8
9 <inputs>
10 <param name="i" type="data" label="Genotypes for analysis from your current history datasets"
11 size="132" format="pbed" />
12 <param name='title' type='text' value='rgTDT' label="Title for the output to remind you what you did" size="80"/>
13 </inputs>
14
15 <outputs>
16 <data format="tabular" name="out_file1" label="${title}_rgTDT.xls"/>
17 <data format="gff" name="gffout" label="${title}_rgTDT.gff"/>
18 <data format="txt" name="logf" label="${title}_rgTDTlog.txt"/>
19 </outputs>
20
21 <tests>
22 <test>
23 <param name='i' value='tinywga' ftype='pbed' >
24 <metadata name='base_name' value='tinywga' />
25 <composite_data value='tinywga.bim' />
26 <composite_data value='tinywga.bed' />
27 <composite_data value='tinywga.fam' />
28 <edit_attributes type='name' value='tinywga' />
29 </param>
30 <param name='title' value='rgTDTtest1' />
31 <output name='out_file1' file='rgTDTtest1_TDT.xls' ftype='tabular' compare="diff"/>
32 <output name='gffout' file='rgTDTtest1_TDT_topTable.gff' ftype='gff' compare="diff" />
33 <output name='logf' file='rgTDTtest1_TDT_log.txt' ftype='txt' lines_diff='79'/>
34 </test>
35 </tests>
36
37
38 <help>
39
40 .. class:: infomark
41
42 **Attribution**
43
44 This tool relies on the work of many people. It uses Plink http://pngu.mgh.harvard.edu/~purcell/plink/ for
45 analysis, and the R http://cran.r-project.org/ for graphics respectively.
46
47 This implementation is a Galaxy tool wrapper around these third party applications.
48 It was originally designed and written for family based data from the CAMP Illumina run of 2007 by
49 ross lazarus (ross.lazarus@gmail.com) and incorporated into the rgenetics toolkit.
50
51 Rgenetics merely exposes them, wrapping Plink so you can use it in Galaxy.
52
53 -----
54
55 .. class:: infomark
56
57 **Syntax**
58
59 - **Genotype file** is the input family data chosen from available library compressed files
60 - **Format** determines how your data will be returned to your Galaxy workspace - the gg format is strongly recommended
61
62 -----
63
64 .. class:: infomark
65
66 **Summary**
67
68 This tool will perform the standard transmission distortion analyses suitable for
69 nuclear families and a simple binary "affected" phenotype
70
71 If you don't see the genotype data set you want here, it can be imported using one of the methods available from
72 the Galaxy Get Data tool page.
73
74 Outputs will include a GFF toptable with a link to view at UCSC if you want to see your
75 results as a fully fledged UCSC track.
76
77 Finally, if you can't live without
78 spreadsheet data, choose the .xls tab delimited format. It's not a stupid binary excel file. Just a plain old tab delimited
79 one with a header. Fortunately excel is dumb enough to open these without much protest.
80
81
82 ----
83
84 .. class:: infomark
85
86 **Attribution**
87
88 This Galaxy tool relies on Plink (see Plinksrc_) to test TDT models.
89
90 So, we rely on the author (Shaun Purcell) for the documentation you need specific to those settings - they are very nicely documented - see
91 DOC_
92
93 Tool and Galaxy datatypes originally designed and written for the Rgenetics
94 series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus@gmail.com)
95
96 Copyright Ross Lazarus March 2007
97 This Galaxy wrapper is released licensed under the LGPL_ but is about as useful as a chocolate teapot without Plink which is GPL.
98
99 I'm no lawyer, but it looks like you got GPL if you use this software. Good luck.
100
101 .. _Plinksrc: http://pngu.mgh.harvard.edu/~purcell/plink/
102
103 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
104
105 .. _DOC: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#tdt
106
107 </help>
108 </tool>