Mercurial > repos > iuc > gemini_burden

annotate gemini_burden.xml @ 0:e799c1a6854b draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:51:59 -0500
parents
children c70d79e0eed7
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0
e799c1a6854b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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1 <tool id="gemini_@BINARY@" name="GEMINI @BINARY@" version="@VERSION@.0">
e799c1a6854b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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2 <description>perform sample-wise gene-level burden calculations</description>
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3 <macros>
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4 <import>gemini_macros.xml</import>
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5 <token name="@BINARY@">burden</token>
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6 </macros>
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7 <expand macro="requirements" />
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8 <expand macro="stdio" />
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9 <expand macro="version_command" />
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10 <command>
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11 <![CDATA[
e799c1a6854b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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12 gemini @BINARY@
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13 --cases $cases
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14 --controls $controls
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15 $save_tscores
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16 $nonsynonymous
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17 $calpha
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18 --permutations $permutations
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19 #if float( str($min_aaf) ) >= 0.0:
e799c1a6854b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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20 --min-aaf $min_aaf
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21 #end if
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22 #if float( str($max_aaf) ) >= 0.0:
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23 --max-aaf $max_aaf
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24 #end if
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25 "${ infile }"
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26 > "${ outfile }"
e799c1a6854b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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27 ]]>
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28
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29 </command>
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30 <inputs>
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31 <expand macro="infile" />
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32
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33 <param name="cases" type="text" value="" label="Space separated list of cases for association testing" help="(--cases)"/>
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34 <param name="controls" type="text" value="" label="Space separated list of controls for association testing" help="(--controls)"/>
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35
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36 <param name="save_tscores" type="boolean" truevalue="--save_tscores" falsevalue="" checked="False"
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37 label="Save the permuted T-scores in the output file" help="(--save_tscores)"/>
e799c1a6854b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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38
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39 <param name="nonsynonymous" type="boolean" truevalue="--nonsynonymous" falsevalue="" checked="False"
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40 label="Count all nonsynonymous variants as contributing burden" help="(--nonsynonymous)"/>
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41 <param name="calpha" type="boolean" truevalue="--calpha" falsevalue="" checked="False"
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42 label="Run the C-alpha association test" help="(--calpha)"/>
e799c1a6854b planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/gemini commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
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43 <param name="min_aaf" type="float" value="-1" label="The min. alt. allele frequency for a variant to be included"
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44 help="(--min-aaf)">
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45 <!--validator type="in_range" min="0.0"/-->
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46 </param>
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47 <param name="max_aaf" type="float" value="-1" label="The max. alt. allele frequency for a variant to be included"
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48 help="(--max-aaf)">
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49 <!--validator type="in_range" min="0.0"/-->
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50 </param>
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51
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52 <param name="permutations" type="integer" value="1000" label="Number of permutations to run for the C-alpha test"
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53 help="(--permutations)">
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54 <validator type="in_range" min="0"/>
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55 </param>
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56
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57 </inputs>
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58 <outputs>
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59 <data name="outfile" format="tabular" />
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60 </outputs>
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61 <tests>
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62 <test>
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63 <param name="infile" value="gemini_burden_input.db" ftype="gemini.sqlite" />
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64 <param name="controls" value="M10475 M10478" />
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65 <param name="cases" value="M10500 M128215" />
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66 <param name="calpha" value="True" />
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67 <output name="outfile" file="gemini_burden_result.tabular" />
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68 </test>
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69 </tests>
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70 <help><![CDATA[
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71 **What it does**
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72
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73 Burden performs sample-wise gene-level burden calculations.
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74
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75 The burden tool provides a set of utilities to perform burden summaries on a per-gene, per sample basis. By default, it outputs a table of gene-wise counts of all high impact variants in coding regions for each sample:
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76
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77 GEMINI burden example::
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78
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79 gene M10475 M10478 M10500 M128215
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80 WDR37 2 2 2 2
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81 CTBP2 0 0 0 1
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82 DHODH 1 0 0 0
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83
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84 **Setting examples**
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85
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86 **--nonsynonymous**
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87
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88 If you want to be a little bit less restrictive, you can include all non-synonymous variants instead.
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89
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90 GEMINI output with setting --nonsynonymous::
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91
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92 gene M10475 M10478 M10500 M128215
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93 SYCE1 0 1 1 0
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94 WDR37 2 2 2 2
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95 CTBP2 0 0 0 1
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96 ASAH2C 2 1 1 0
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97 DHODH 1 0 0 0
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98
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99 **--calpha**
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100
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101 If your database has been loaded with a PED file describing case and control samples, you can calculate the c-alpha statistic for cases vs. control.
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102
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103 GEMINI output with setting --calpha::
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104
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105 gene T c Z p_value
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106 SYCE1 -0.5 0.25 -1.0 0.841344746069
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107 WDR37 -1.0 1.5 -0.816496580928 0.792891910879
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108 CTBP2 0.0 0.0 nan nan
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109 ASAH2C -0.5 0.75 -0.57735026919 0.718148569175
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110 DHODH 0.0 0.0 nan nan
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111
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112 To calculate the **P-value** using a permutation test, use the --permutations option, specifying the number of permutations of the case/control labels you want to use.
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113
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114 **--min-aaf and --max-aaf for --calpha**
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115
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116 By default, all variants affecting a given gene will be included in the C-alpha computation. However, one may establish alternate allele frequency boundaries for the variants included using the --min-aaf and --max-aaf options.
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117
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118 Used settings:
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119
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120 - -calpha test.burden.db
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121 - -min-aaf 0.0
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122 - -max-aaf 0.01
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123 - -cases
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124 - -controls for --calpha
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125
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126 If you do not have a PED file loaded, or your PED file does not follow the standard PED phenotype encoding format you can still perform the c-alpha test, but you have to specify which samples are the control samples and which are the case samples.
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127
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128 Used settings:
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129
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130 - -controls M10475 M10478
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131 - -cases M10500 M128215
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132 - -calpha
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133
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134 Output::
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135
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136 gene T c Z p_value
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137 SYCE1 -0.5 0.25 -1.0 0.841344746069
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138 WDR37 -1.0 1.5 -0.816496580928 0.792891910879
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139 CTBP2 0.0 0.0 nan nan
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140 ASAH2C -0.5 0.75 -0.57735026919 0.718148569175
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141 DHODH 0.0 0.0 nan nan
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142
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143 **--nonsynonymous --calpha**
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144
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145 If you would rather consider all nonsynonymous variants for the C-alpha test rather than just the medium and high impact variants, add the --nonsynonymous flag.
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146
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147
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148 ]]></help>
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149 <expand macro="citations">
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150 <citation type="doi">10.1371/journal.pgen.1001322</citation><!-- c-alpha citation -->
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151 </expand>
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152 </tool>