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