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annotate abims_anova.xml @ 6:0f8a79085317 draft

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planemo upload for repository https://github.com/workflow4metabolomics/anova commit dec8e4ddb5cedacc334b8397ac1549c8701d623b
author lecorguille
date Thu, 26 Oct 2017 09:30:37 -0400
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1 <tool id="abims_anova" name="Anova" version="1.1.4">
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3 <description>N-way anova. With ou Without interactions</description>
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5 <requirements>
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6 <requirement type="package" version="1.1_4">r-batch</requirement>
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7 </requirements>
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9 <stdio>
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10 <exit_code range="1:" level="fatal" />
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11 </stdio>
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13 <command>
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14 Rscript $__tool_directory__/abims_anova.r file '$input' sampleinfo '$sampleinfo' mode '$mode'
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15 condition "c('$condition_1'
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16 #for $i, $s in enumerate( $conditions )
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17 ,'${s.condition}'
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18 #end for
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19 )"
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20 interaction $interaction
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21 method $method
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22 threshold $threshold
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23 selection_method $selection_method
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24 sep '$sep'
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25 dec '$dec'
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26 outputdatapvalue '$dataMatrixPValue'
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27 outputdatafiltered '$dataMatrixFiltered'
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28 </command>
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30 <inputs>
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31 <param name="input" type="data" label="Data Matrix file" format="tabular" help="Matrix of numeric data with headers." />
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32 <param name="sampleinfo" type="data" label="Sample Metadata file" format="tabular" help="Tabular file with the data metadata : one sample per line and at least two columns : ids and one condition" />
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34 <param name="mode" type="select" help="Perform the anova tests on column/row" format="text" optional="true">
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35 <label>Mode</label>
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36 <option value="row">row</option>
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37 <option value="column">column</option>
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38 </param>
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40 <param name="condition_1" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" optional="false" />
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41 <repeat name="conditions" title="Conditions for N-ways anova">
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42 <param name="condition" type="text" label="Condition" value="" help="The column name of the condition. ex: hour or treatment" />
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43 </repeat>
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45 <param name="interaction" type="boolean" label="Enable interaction response p-values" truevalue="T" falsevalue="F" help="Used if more than 1 conditon. The anova will produse p-value according to the interaction between your condition (ex: condition1:conditions2, condition1:conditions3, condition2:conditions3 and condition1:condition2:conditions3)" />
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47 <param name="method" type="select" help="Method used to apply a correction on the pvalue because of the number of test" >
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48 <label>PValue adjusted method</label>
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49 <option value="BH">BH</option>
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50 <option value="holm">holm</option>
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51 <option value="bonferroni">bonferroni</option>
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52 <option value="hochberg">hochberg</option>
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53 <option value="hommel">hommel</option>
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54 <option value="BY">BY</option>
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55 <option value="fdr">fdr</option>
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56 <option value="none">none</option>
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57 </param>
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59 <param name="threshold" type="float" label="Threshold" value="0.01" help="max adjusted p.value accepted" />
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61 <param name="selection_method" type="select" help="Intersection: all condition p-value must be under the threshold. Union: at least condition p-value must be under the threshold. ">
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62 <label>Selection method</label>
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63 <option value="intersection" selected="true">intersection / strong</option>
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64 <option value="union">union / weak</option>
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65 </param>
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67 <param name="sep" type="select" format="text">
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68 <label>Separator of columns</label>
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69 <option value="tabulation">tabulation</option>
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70 <option value="semicolon">;</option>
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71 <option value="comma">,</option>
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72 </param>
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74 <param name="dec" type="text" label="Decimal separator" value="." help="" />
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76 </inputs>
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78 <outputs>
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79 <data name="dataMatrixPValue" format_source="input" label="${input.name}_anova_pvalue.${input.ext}"/>
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80 <data name="dataMatrixFiltered" format_source="input" label="${input.name}_anova_filtered.${input.ext}"/>
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81 </outputs>
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83 <tests>
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84 <test>
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85 <param name="input" value="dataMatrix.tsv"/>
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86 <param name="sampleinfo" value="sampleMetadata.tsv"/>
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87 <param name="mode" value="row"/>
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88 <param name="condition_1" value="age"/>
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89 <param name="conditions_0|condition" value="gender"/>
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90 <param name="interaction" value="F"/>
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91 <param name="method" value="BH"/>
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92 <param name="threshold" value="0.05"/>
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93 <param name="selection_method" value="union"/>
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94 <param name="sep" value="tabulation"/>
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95 <param name="dev" value="."/>
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96 <output name="dataMatrixPValue" file="dataMatrix.tsv_anova_pvalue.tabular" />
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97 <output name="dataMatrixFiltered" file="dataMatrix.tsv_anova_filtered.tabular" />
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98 </test>
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99 </tests>
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100
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101 <help>
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102
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103 .. class:: infomark
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104
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105 **Authors** Gildas Le Corguille ABiMS - UPMC/CNRS - Station Biologique de Roscoff - gildas.lecorguille|at|sb-roscoff.fr
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106
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107 ---------------------------------------------------
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108
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109 =====
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110 Anova
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111 =====
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113 -----------
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114 Description
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115 -----------
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116
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117 Analysis of variance (ANOVA) is used to analyze the differences between group means and their associated procedures,
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118 in which the observed variance in a particular variable is partitioned into components attributable to different sources of variation.
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119
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121
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122 -----------
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123 Input files
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124 -----------
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125
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126 +---------------------------+------------+
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127 | Parameter : num + label | Format |
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128 +===========================+============+
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129 | 1 : Data Matrix file | Tabular |
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130 +---------------------------+------------+
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131 | 2 : Sample Metadata file | Tabular |
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132 +---------------------------+------------+
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136 ------------
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137 Output files
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138 ------------
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139
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142 ***.anova_pvalue.tabular**
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143
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144 | A tabular file which represents for each metabolite (row), the value of the intensity in each sample (column) + two columns (aovPValue and aovAdjPValue).
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145
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146 ***.anova_filtered.tabular**
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148 | The tabular file xset.anova_pvalue.tabular containing only the metabolites that have been filtered by aovAdjPValue.
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149
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151 ------
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152
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153 .. class:: infomark
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154
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155 The outputs ***.anova_filtered.tabular** or ***.anova_pvalue.tabular** are tabular files. You can continue your analysis using it in the following tools:
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156
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157 | PCA
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158 | Hierarchical Clustering
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161
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162 ---------------------------------------------------
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164 ---------------
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165 Working example
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166 ---------------
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169 Input files
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170 -----------
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171
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172 **>A part of an example of Data Matrix file input**
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175 +--------+------------------+----------------+
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176 | Name | Bur-eH_FSP_12 | Bur-eH_FSP_24 |
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177 +========+==================+================+
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178 |M202T601| 91206595.7559783 |106808979.08546 |
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179 +--------+------------------+----------------+
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180 |M234T851| 27249137.275504 |28824971.3177926|
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181 +--------+------------------+----------------+
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183 **>A part of an example of Sample Metadata file input**
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186 +---------------------------+------------+------------+------------+
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187 | Sample name | class | time | batch |
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188 +===========================+============+============+============+
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189 | Bur-eH_FSP_12 | Bur-eH | 12 | 1 |
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190 +---------------------------+------------+------------+------------+
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191 | Bur-eH_FSP_24 | Bur-eH | 24 | 1 |
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192 +---------------------------+------------+------------+------------+
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193 | Bur-NI_FSP_12 | Bur-NI | 12 | 2 |
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194 +---------------------------+------------+------------+------------+
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195 | Bur-NI_FSP_24 | Bur-NI | 24 | 2 |
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196 +---------------------------+------------+------------+------------+
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198 Parameters
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199 ----------
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201 | Mode -> **row**
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202 | column name of condition -> **class**
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203 | Separator of columns: -> **tabulation**
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204 | Decimal separator -> **.**
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205 | PValue adjusted method -> **BH**
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206 | Threshold -> **0.001**
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209
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210 Output files
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211 ------------
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213 **Part of an example of xset.anova_filtered.tabular:**
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214
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215 .. image:: anova_pvalue.png
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216
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217 **Part of an example of xset.anova_pvalue.tabular:**
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218
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219 .. image:: anova_filtered.png
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221
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222 ---------------------------------------------------
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223
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224
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225 ---------------------------
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226 Position in workflow4metabo
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227 ---------------------------
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228
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229
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230 **Upstream tools**
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232 +---------------------------+----------------------------------------+--------+------------------------+
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233 | Name | Output file | Format | parameter |
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234 +===========================+========================================+========+========================+
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235 |CAMERA.annotateDiffreport |xset.annotatediffreport.data_matrix.tsv | Tabular| Data table file |
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236 +---------------------------+----------------------------------------+--------+------------------------+
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237 |xcms.xcmsSet |sample_info.tab | Tabular| sample info table file |
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238 +---------------------------+----------------------------------------+--------+------------------------+
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239
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240
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241 **Downstream tools**
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242
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243 +---------------------------+---------------------------------------------------------+--------+
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244 | Name | Output file | Format |
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245 +===========================+=========================================================+========+
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246 |PCA |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular|
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247 +---------------------------+---------------------------------------------------------+--------+
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248 |Hierarchical Clustering |xset.anova_pvalue.tabular OR xset.anova_filtered.tabular | Tabular|
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249 +---------------------------+---------------------------------------------------------+--------+
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250
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251
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252 **General schema of the metabolomic workflow**
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253
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254 .. image:: anova_workflow.png
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255
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256 </help>
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257
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258 <citations>
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259 <citation type="bibtex">@ARTICLE{fisher,
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260 author = {Ronald A. Fisher},
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261 title = {The Correlation between Relatives on the Supposition of Mendelian Inheritance},
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262 journal = {Philosophical Transactions of the Royal Society of Edinburgh},
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263 year = {1918},
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264 volume = {52},
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265 pages = {399-433}
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266 }</citation>
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267 </citations>
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268
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269 </tool>