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1 <tool id="rgCaCo1" name="Case Control:">
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2 <description>for unrelated subjects</description>
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3 <command interpreter="python">
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4 rgCaCo.py '$i.extra_files_path/$i.metadata.base_name' "$title" '$out_file1' '$logf' '$logf.files_path' '$gffout'
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5 </command>
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6 <inputs>
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7 <param name="i" type="data" label="RGenetics genotype data from your current history"
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8 format="pbed" />
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9 <param name='title' type='text' size="132" value='CaseControl' label="Title for this job"/>
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10
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11 </inputs>
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12
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13 <outputs>
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14 <data format="tabular" name="out_file1" label="${title}_rgCaCo.xls" />
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15 <data format="txt" name="logf" label="${title}_rgCaCo.log"/>
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16 <data format="gff" name="gffout" label="${title}_rgCaCoTop.gff" />
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17 </outputs>
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18 <tests>
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19 <test>
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20 <param name='i' value='tinywga' ftype='pbed' >
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21 <metadata name='base_name' value='tinywga' />
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22 <composite_data value='tinywga.bim' />
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23 <composite_data value='tinywga.bed' />
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24 <composite_data value='tinywga.fam' />
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25 <edit_attributes type='name' value='tinywga' />
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26 </param>
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27 <param name='title' value='rgCaCotest1' />
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28 <output name='out_file1' file='rgCaCotest1_CaCo.xls' ftype='tabular' compare='diff' />
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29 <output name='logf' file='rgCaCotest1_CaCo_log.txt' ftype='txt' compare='diff' lines_diff='20' />
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30 <output name='gffout' file='rgCaCotest1_CaCo_topTable.gff' ftype='gff' compare='diff' />
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31 </test>
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32 </tests>
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33 <help>
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34
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35 .. class:: infomark
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36
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37 **Syntax**
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38
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39 - **Genotype file** is the input case control data chosen from available library Plink binary files
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40 - **Map file** is the linkage format .map file corresponding to the genotypes in the Genotype file
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41 - **Type of test** is the kind of test statistic to report such as Armitage trend test or genotype test
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42 - **Format** determines how your data will be returned to your Galaxy workspace
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43
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44 -----
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45
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46 **Summary**
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47
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48 This tool will perform some standard statistical tests comparing subjects designated as
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49 affected (cases) and unaffected subjects (controls). To avoid bias, it is important that
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50 controls who had been affected would have been eligible for sampling as cases. This may seem
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51 odd, but it requires that the cases and controls are drawn from the same sampling frame.
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52
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53 The armitage trend test is robust to departure from HWE and so very attractive - after all, a real disease
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54 mutation may well result in distorted HWE at least in cases. All the others are susceptible to
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55 bias in the presence of HWE departures.
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56
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57 All of these tests are exquisitely sensitive to non-differential population stratification in cases
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58 compared to controls and this must be tested before believing any results here. Use the PCA method for
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59 100k markers or more.
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60
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61 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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62 the Galaxy Get Data tool page.
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63
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64 Output format can be UCSC .bed if you want to see your
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65 results as a fully fledged UCSC track. A map file containing the chromosome and offset for each marker is required for
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66 writing this kind of output.
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67 Alternatively you can use .gg for the UCSC Genome Graphs tool which has all of the advantages
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68 of the the .bed track, plus a neat, visual front end that displays a lot of useful clues.
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69 Either of these are a very useful way of quickly getting a look
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70 at your data in full genomic context.
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71
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72 Finally, if you can't live without
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73 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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74 one with a header. Fortunately excel is dumb enough to open these without much protest.
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75
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76
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77 -----
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78
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79 .. class:: infomark
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80
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81 **Attribution**
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82
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83 This Galaxy tool relies on Plink (see Plinksrc_) to test Casae Control association models.
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84
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85 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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86 DOC_
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87
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88 Tool and Galaxy datatypes originally designed and written for the Rgenetics
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89 series of whole genome scale statistical genetics tools by ross lazarus (ross.lazarus@gmail.com)
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90
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91 Copyright Ross Lazarus March 2007
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92 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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93
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94 I'm no lawyer, but it looks like you got GPL if you use this software. Good luck.
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95
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96 .. _Plinksrc: http://pngu.mgh.harvard.edu/~purcell/plink/
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97
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98 .. _LGPL: http://www.gnu.org/copyleft/lesser.html
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99
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100 .. _DOC: http://pngu.mgh.harvard.edu/~purcell/plink/anal.shtml#cc
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101
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102 </help>
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103 </tool>
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