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1 <tool id="fakePhe1" name="Null phenotypes">
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2 <description>for testing</description>
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3 <command interpreter="python">rgfakePhe.py '$infile1.extra_files_path/$infile1.metadata.base_name'
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4 "$title1" '$ppheout' '$ppheout.files_path' '$script_file'
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5 </command>
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6 <inputs>
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7 <page>
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8 <param name="infile1"
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9 type="data" format="pbed,lped"
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10 label="Pedigree from Dataset" />
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11 <param name="title1" type="text"
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12 value="My null phenos" size="60"
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13 label="Title for outputs"/>
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14 <param name="dbkey" type="hidden" value='hg18' />
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15 </page>
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16 <page>
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17 <repeat name="fakePhe" title="Phenotypes to simulate under the Null">
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18 <param name="pName" type="text" label="Phenotype Name">
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19 </param>
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20 <conditional name="series">
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21 <param name="phetype" type="select" label="Phenotype Distribution">
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22 <option value="rnorm" selected="true">Random Normal variate</option>
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23 <option value="unif">Random Uniform variate</option>
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24 <option value="rgamma">Random Gamma variate</option>
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25 <option value="weibull">Random Weibull variate</option>
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26 <option value="exponential">Random exponential variate</option>
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27 <option value="poisson">Random Poisson variate</option>
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28 <option value="cat">Random categorical choice</option>
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29 </param>
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30 <when value="poisson">
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31 <param name="lamb" type="integer" value="2" label="Lambda (mean and variance)" />
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32 </when>
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33 <when value="rnorm">
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34 <param name="Mean" type="float" value="0.0" label="Mean" />
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35 <param name="SD" type="float" label="SD" value="1.0"/>
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36 </when>
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37 <when value="exponential">
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38 <param name="Mean" type="float" value="1.0" label="Mean" help="lambda for the exponential will be 1.0/Mean" />=
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39 </when>
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40 <when value="rgamma">
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41 <param name="Alpha" type="float" value="10" label="Alpha">
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42 </param>
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43 <param name="Beta" type="float" label="Beta" value="1.0">
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44 </param>
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45 </when>
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46 <when value="weibull">
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47 <param name="Alpha" type="float" value="10" label="Alpha">
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48 </param>
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49 <param name="Beta" type="float" label="Beta" value="1.0">
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50 </param>
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51 </when>
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52 <when value="unif">
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53 <param name="low" type="float" value="0.0" label="Lowest uniform value">
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54 </param>
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55 <param name="hi" type="float" label="Highest uniform value" value="1.0"
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56 help="A uniform value will be generated from the range specified (low to high) - eg 0.0 to 1.0">
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57 </param>
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58 </when>
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59 <when value="cat">
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60 <param name="values" type="text" value="A,B,C" label="Comma separated values to choose from"
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61 help = "Each of the comma separated values will have an equal probability of being chosen - eg 'A1,A2,B1,B2'">
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62 </param>
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63 </when>
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64 </conditional>
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65 </repeat>
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66 </page>
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67 </inputs>
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68 <outputs>
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69 <data format="pphe" name="ppheout" metadata_source="infile1" />
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70 </outputs>
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71 <configfiles>
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72 <configfile name="script_file">
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73 #for $n, $f in enumerate($fakePhe)
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74 #if $f.series.phetype=='rnorm'
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75 {'pN':'$f.pName','pT':'rnorm','pP':"{'Mean':'$f.series.Mean', 'SD':'$f.series.SD'}"}
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76 #elif $f.series.phetype=='rgamma'
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77 {'pN':'$f.pName','pT':'rgamma','pP':"{'Alpha':'$f.series.Alpha', 'Beta':'$f.series.Beta'}"}
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78 #elif $f.series.phetype=='poisson'
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79 {'pN':'$f.pName','pT':'poisson','pP':"{'lamb':'$f.series.lamb',}"}
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80 #elif $f.series.phetype=='exponential'
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81 {'pN':'$f.pName','pT':'exponential','pP':"{'Mean':'$f.series.Mean',}"}
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82 #elif $f.series.phetype=='weibull'
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83 {'pN':'$f.pName','pT':'weibull','pP':"{'Alpha':'$f.series.Alpha', 'Beta':'$f.series.Beta'}"}
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84 #elif $f.series.phetype=='cat'
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85 {'pN':'$f.pName','pT':'$f.series.phetype','pP':"{'values':'$f.series.values'}"}
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86 #elif $f.series.phetype=='unif'
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87 {'pN':'$f.pName','pT':'$f.series.phetype','pP':"{'low':'$f.series.low','hi':'$f.series.hi'}"}
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88 #end if
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89 #end for
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90 </configfile>
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91 </configfiles>
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92 <help>
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93 .. class:: infomark
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94
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95 This tool allows you to generate an arbitrary (sort of)
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96 synthetic phenotype file with measurements drawn from normal,
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97 gamma, weibull, exponential, uniform or categorical distributions. These are for testing under
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98 the null hypothesis of no association - the values are random but
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99 from user specified distributions.
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100
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101 Two output files will appear - one for FBAT and the other for Plink since unfortunately,
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102 they have slightly differing requirements for the header row.
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103
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104 -----
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105
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106 .. class:: warningmark
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107
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108 This tool is very experimental
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109
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110 -----
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111
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112 - **Pedigree** is a library pedigree file - the id's will be used in the synthetic null phenotypes
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113 - **Title** is a name to give to the output phenotype file
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114
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115 On the next page, you can add an unlimited number of various kinds of phenotypes including choices for
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116 categorical ones or distributions with specific parameters
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117
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118 Just keep using the "Add new phenotype" button to add new specifications until you're done.
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119 Use the Execute button to run the program and generate the null phenotype data.
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120 The new files will be available on the drop down lists for appropriate tools - eg the
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121 FBAT format one will be available if you run the FBAT modelling tool.
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122
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123 **Attribution**
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124 Originally designed and written for the Rgenetics
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125 series of Galaxy tools, and
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126 copyright Ross Lazarus 2007 (ross period lazarus at gmail period com)
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127 Licensed under the terms of the LGPL
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128 as documented http://www.gnu.org/licenses/lgpl.html
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129
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130 </help>
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131 </tool>
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