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1 <tool id="rgManQQ1" name="Manhattan/QQ:" version="1.0.3">
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2 <code file="rgManQQ_code.py"/>
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3
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4 <description>Plots for WGA P values</description>
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5
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6 <command interpreter="python">
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7 rgManQQ.py '$i' "$name" '$out_html' '$out_html.files_path' '$chrom_col' '$offset_col' '$pval_col' '$grey'
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8 </command>
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9
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10 <inputs>
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11 <page>
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12 <param name="i" type="data" label="Tabular data from your current history"
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13 format="tabular" refresh_on_change="true"/>
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14 </page>
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15 <page>
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16 <param name='name' type='text' size="132" value='Manhattan and QQ plots' label="Title for this job"/>
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17 <param name="pval_col" type='select' size="5" label = 'P value (0-1) column in input file'
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18 dynamic_options="get_phecols(i,False,'pval')" refresh_on_change="true" multiple="true"
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19 help="(Select multiple P value columns for multiple plots holding down the [Ctrl] key as you click)" />
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20 <param name="chrom_col" type='select' label = 'Chromosome column in input file'
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21 help='Select "None" if chromosome not available or no Manhattan plot required'
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22 dynamic_options="get_phecols(i,True,'chr')" />
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23 <param name="offset_col" type='select' label = 'Base pair offset column in input file'
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24 help='Select "None" if offset not available or no Manhattan plot required'
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25 dynamic_options="get_phecols(i,True,'offs')" />
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26 <param name="grey" type="boolean" checked="false" truevalue="true" falsevalue="false"
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27 label="Grey scale for Manhattan plot (default is colour"/>
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28 </page>
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29 </inputs>
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30
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31 <outputs>
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32 <data format="html" name="out_html" />
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33 </outputs>
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34 <options refresh="True"/>
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35
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36 <tests>
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37 <test>
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38 <param name='i' value='smallwgaP.xls' ftype='tabular' >
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39 </param>
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40 <param name='name' value='rgManQQtest1' />
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41 <param name='pval_col' value='7' />
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42 <param name='chrom_col' value='1' />
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43 <param name='offset_col' value='2' />
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44 <param name='grey' value='0' />
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45 <output name='out_html' file='rgtestouts/rgManQQ/rgManQQtest1.html' ftype='html' lines_diff='60'>
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46 <extra_files type="file" name='Allelep_manhattan.png' value='rgtestouts/rgManQQ/Allelep_manhattan.png' compare="sim_size"
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47 delta = "20000"/>
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48 <extra_files type="file" name='Allelep_qqplot.png' value='rgtestouts/rgManQQ/Allelep_qqplot.png' compare="sim_size"
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49 delta = "20000" />
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50 <extra_files type="file" name='rgManQQtest1.R' value='rgtestouts/rgManQQ/rgManQQtest1.R' compare="diff" lines_diff="160"/>
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51 </output>
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52 </test>
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53 </tests>
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54 <help>
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55
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56 .. class:: infomark
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57
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58 **Syntax**
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59
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60 - **Tabular Data** is a tab delimited header file with chromosome, offset and p values to be plotted
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61 - **Chromosome Column** is the column in that data containing the chromosome as an integer
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62 - **Offset Column** contains the offset within the chromosome
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63 - **P Value Column** contains the (untransformed) p values at that locus - choose multiple columns if needed
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64
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65 NOTE - plotting millions of p values may take tens of minutes depending on
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66 how busy the server is - be patient please.
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67
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68 -----
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69
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70 .. class:: infomark
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71
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72 **Summary**
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73
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74 This tool will create a qq plot and a Manhattan plot for one or more GWA P value columns from a tabular
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75 dataset. For Manhattan plots, the data must include the chromosome (eg use 23,24,25 for x,y,mt...) and
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76 offset. Many analysis files contain the required fields but even without chromosome and offset, a qq plot
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77 can be created.
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78
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79 -----
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80
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81 .. class:: infomark
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82
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83 **Explanation**
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84
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85 A "Manhattan" plot shows -log10 p values ordered by offset and by chromosome. Regions with interestingly
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86 improbable p values are above the red line which is drawn at the Bonferroni FWER control level (0.05/n
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87 where n is the number of tests - this is highly conservative for correlated SNPs typical of GWA)
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88
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89 .. image:: ./static/images/Armitagep_manhattan.png
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90
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91 A quantile-quantile (QQ) plot is a good way to see systematic departures from the null expectation of
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92 uniform p-values from a genomic analysis. If the QQ plot shows departure from the null (ie a uniform 0-1
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93 distribution), you hope that this will be in the very smallest p-values suggesting that there might be some
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94 interesting results to look at. A log scale will help emphasise departures from the null at low p values
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95 more clear
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96
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97 .. image:: ./static/images/Armitagep_qqplot.png
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98
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99 -----
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100
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101 .. class:: infomark
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102
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103 **Attribution**
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104
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105 This is a Galaxy tool written by Ross Lazarus. It relies on
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106 ggplot2, an R package from hadley wickham and some
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107 R code for manhattan and qq plots using ggplot2,
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108 borrowed from Stephen Turner found at http://GettingGeneticsDone.blogspot.com/
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109
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110 copyright Ross Lazarus 2010
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111 Licensed under the terms of the LGPL as documented http://www.gnu.org/licenses/lgpl.html
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112 but is about as useful as a chocolate teapot without R and Galaxy which all have a
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113 twisty maze of little licenses, all different.
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114
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115 I'm no lawyer, but it looks like at least LGPL if you create derived works from this code.
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116 Good luck.
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117
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118 </help>
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119 </tool>
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