Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov.xml @ 13:2ae2d26e3270 draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
author eschen42
date Wed, 12 Dec 2018 09:20:02 -0500
parents ddaf84e15d06
children 90708fdbc22d
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1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.17">
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2 <description>OPLS-DA Contrasts of Univariate Results</description>
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3 <macros>
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4 <xml name="paramPairSigFeatOnly">
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5 <param name="pairSigFeatOnly" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
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6 label="Retain only pairwise-significant features"
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7 help="When this option is set to 'Yes', analysis will be performed including only features scored by the univariate test as differing significantly for the pair of levels being contrasted; when set to 'No', any feature that varies significantly across all levels will be included (i.e., exclude only features not scored by the univariate test as significantly varying when all levels are considered). See examples below." />
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8 </xml>
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9 <xml name="cplots">
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10 <param name="cplot_y" label="C-plot Y-axis" type="select" help="Choose the Y-axis for C-plots.">
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11 <option value="correlation">Plot VIP versus correlation</option>
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12 <option value="covariance">Plot VIP versus covariance</option>
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13 </param>
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14 <param name="cplot_p" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
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15 label="Produce predictor C-plot"
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16 help="When this option is set to 'Yes', correlation will be plotted against vip4 for predictor loadings." />
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17 <param name="cplot_o" type="boolean" checked="true" truevalue="TRUE" falsevalue="FALSE"
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18 label="Produce orthogonal C-plot"
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19 help="When this option is set to 'Yes', correlation will be plotted against vip4 for orthogonal loadings." />
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20 <param name="fdr_features" type="text" value="ALL"
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21 label="How many features for p-value calculation?"
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22 help="Specify how many features should be used to perform family-wise error rate adjustment of p-values for covariance and correlation. If you were to eliminate features from the data matrix based on significance criteria prior to running this tool, you would want to include them in the count here to avoid underestimating the p-value. Specify 'ALL' to signify that all features that could impact p-value calculation are included in the data matrix."/>
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23 </xml>
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24 </macros>
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25 <requirements>
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26 <requirement type="package">r-base</requirement>
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27 <requirement type="package">r-batch</requirement>
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28 <requirement type="package" version="1.10.0">bioconductor-ropls</requirement>
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29 </requirements>
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30 <command detect_errors="aggressive"><![CDATA[
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31 Rscript '$__tool_directory__/w4mcorcov_wrapper.R'
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32 dataMatrix_in '$dataMatrix_in'
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33 sampleMetadata_in '$sampleMetadata_in'
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34 variableMetadata_in '$variableMetadata_in'
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35 facC '$facC'
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36 #if str( $signif_test.tesC ) == 'none':
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37 tesC 'none'
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38 pairSigFeatOnly 'FALSE'
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39 #else:
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40 tesC '$signif_test.tesC'
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41 pairSigFeatOnly '$signif_test.pairSigFeatOnly'
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42 #end if
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43 levCSV '$levCSV'
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44 matchingC '$matchingC'
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45 labelFeatures '$labelFeatures'
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46 #if str( $advanced.advancedFeatures ) == 'none':
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47 fdr_features 'ALL'
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48 cplot_p 'FALSE'
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49 cplot_o 'FALSE'
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50 cplot_y 'correlation'
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51 #else if str( $advanced.advancedFeatures ) == 'advanced':
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52 fdr_features '$advanced.fdr_features'
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53 cplot_p '$advanced.cplot_p'
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54 cplot_o '$advanced.cplot_o'
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55 cplot_y '$advanced.cplot_y'
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56 #end if
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57 contrast_detail '$contrast_detail'
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58 contrast_corcov '$contrast_corcov'
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59 contrast_salience '$contrast_salience'
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60 ]]></command>
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61 <inputs>
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62 <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"
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63 help="variables &#10006; samples" />
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64 <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data"
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65 help="sample metadata, one row per sample" />
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66 <param name="variableMetadata_in" format="tabular" label="Variable metadata file (ideally from Univariate)"
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67 type="data" help="variable metadata, one row per variable" />
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68 <param name="facC" type="text"
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69 label="Factor of interest"
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70 help="REQUIRED - The name of the column of sampleMetadata corresponding to the qualitative variable used to define the contrasts. Except when the 'Univariate Significance-test' is set to 'none', this also must be a portion of the column names in the variableMetadata file.">
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71 <sanitizer>
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72 <valid initial="string.letters">
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73 <add preset="string.digits"/>
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74 <add value="&#46;" /> <!-- dot, period -->
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75 <add value="&#95;" /> <!-- underscore -->
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76 <!-- R does not permit dashes in column names; neither does SQL -->
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77 </valid>
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78 </sanitizer>
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79 </param>
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80 <conditional name="signif_test">
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81 <param name="tesC" label="Univariate significance-test" type="select" help="Either 'none' or the name of the statistical test that was run by the 'Univariate' tool to produce the variableMetadata file.">
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82 <option value="none">none - Display all features from variableMetadata (rather than choosing a subset based on significance in univariate testing)</option>
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83 <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option>
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84 <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option>
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85 <option value="wilcoxon">wilcoxon - Wilcoxon rank test (nonparametric test, qualitative factor with exactly 2 levels)</option>
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86 <option value="kruskal">kruskal - Kruskal-Wallis rank test (nonparametric test, qualitative factor with more than 2 levels)</option>
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87 </param>
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88 <when value="none" />
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89 <when value="ttest">
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90 <expand macro="paramPairSigFeatOnly" />
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91 </when>
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92 <when value="anova">
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93 <expand macro="paramPairSigFeatOnly" />
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94 </when>
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95 <when value="wilcoxon">
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96 <expand macro="paramPairSigFeatOnly" />
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97 </when>
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98 <when value="kruskal">
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99 <expand macro="paramPairSigFeatOnly" />
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100 </when>
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101 </conditional>
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102 <param name="levCSV" type="text" value="*" label="Levels of interest"
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103 help="Comma-separated level-names (or comma-separated regular expressions to match level-names) to consider in analysis; must match at least two levels; levels must be non-numeric; may include wild cards or regular expressions. Note that extra space characters will affect results - when 'a,b' is correct, 'a, b' is not equivalent and likely will fail or give different results.">
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104 <sanitizer>
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105 <valid initial="string.letters">
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106 <add preset="string.digits"/>
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107 <add value="&#36;" /> <!-- $ dollar, dollar-sign -->
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108 <add value="&#40;" /> <!-- ( left-paren -->
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109 <add value="&#41;" /> <!-- ) right-paren -->
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110 <add value="&#42;" /> <!-- * splat, asterisk -->
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111 <add value="&#43;" /> <!-- + plus -->
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112 <add value="&#44;" /> <!-- , comma -->
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113 <add value="&#45;" /> <!-- - dash, minus-sign -->
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114 <add value="&#46;" /> <!-- . dot, period -->
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115 <add value="&#58;" /> <!-- : colon -->
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116 <add value="&#59;" /> <!-- ; semi, semicolon -->
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117 <add value="&#63;" /> <!-- ? what, question mark -->
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118 <add value="&#91;" /> <!-- [ l-squib, left-squre-bracket -->
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119 <add value="&#92;" /> <!-- \ whack, backslash -->
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120 <add value="&#93;" /> <!-- ] r-squib, right-squre-bracket -->
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121 <add value="&#94;" /> <!-- ^ hat, caret -->
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122 <add value="&#95;" /> <!-- underscore -->
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123 <add value="&#123;" /> <!-- { l-cube, left-curly-bracket -->
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124 <add value="&#124;" /> <!-- | pipe -->
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125 <add value="&#125;" /> <!-- } r-cube, right-curly-bracket -->
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126 <!-- IMPORTANT - Note that single and double quotes are not part of this list; they have the potential to make the 'command' section insecure or broken. -->
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127 </valid>
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128 </sanitizer>
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129 </param>
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130 <param name="matchingC" label="Level-name matching" type="select" help="How to specify level-names generically. (See help below for details on using wild cards or regular expressions.)">
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131 <option value="none">do no generic matching</option>
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132 <option value="wildcard" selected="true">use wild-cards for matching level-names (default)</option>
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133 <option value="regex">use regular expressions for matching level-names</option>
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134 </param>
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135 <param name="labelFeatures" type="text" value="3"
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136 label="How many features having extreme loadings should be labelled on cov-vs.-cor plot?"
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137 help="Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features or '0' to label no features; this choice has no effect on the OPLS-DA loadings plot."/>
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138 <conditional name="advanced">
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139 <param name="advancedFeatures" type="select"
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140 label="Advanced (C-plots and customized p-value adjustment)"
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141 help="Choose 'Do not include ...' to hides further choices.">
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142 <option value="advanced">Include C-plots and customize p-value adjustment.</option>
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143 <option value="none">Do not include additonal C-plots or customize p-value adjustment.</option>
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144 </param>
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145 <when value="none" />
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146 <when value="advanced">
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147 <expand macro="cplots" />
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148 </when>
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149 </conditional>
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150 </inputs>
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151 <outputs>
0
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152 <!--
2
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153 pdf1: summaries of each contrasts, clearly labelled by level=pair name
0
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154 * first PCA score-plot
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155 * then OPLS score-plot
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156 * then OPLS S-PLOT; color saturation increases with VIP
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157 * then C-plots if requrested
0
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158 -->
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159 <data name="contrast_detail" format="pdf" label="${tool.name}_${variableMetadata_in.name}_detail" />
0
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160 <!--
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161 tsv1: cor and cov table with columns:
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162 * feature-ID
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163 * factor-level 1
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164 * factor-level 2, lexically greater than level 1
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165 * Wiklund_2008 correlation
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166 * Wiklund_2008 covariance
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167 * Galindo_Prieto_2014 VIP for predictive components, VIP[4,p]
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168 * Galindo_Prieto_2014 VIP for orthogonal components, VIP[4,o]
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169 * When filtering on significance of univariate tests,significance of test of null hypothesis that there is no difference between the two classes, i.e, the pair-wise test.
0
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170 -->
8
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171 <data name="contrast_corcov" format="tabular" label="${tool.name}_${variableMetadata_in.name}_corcov" />
0
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172 <!--
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173 tsv2: salience table with columns (experimental feature):
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174 * feature-ID
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175 * Salient level, i.e., for the feature, the class-level having the greatest median intensity
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176 * Salient robust coefficient of variation, i.e., for the feature, the mean absolute deviation of the intensity for the salient level divided by the median intensity for the salient level
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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177 * Salience, i.e., for the feature, the median of the class-level having the greatest intensity divided by the mean of the medians for all class-levels.
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178 -->
8
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179 <data name="contrast_salience" format="tabular" label="${tool.name}_${variableMetadata_in.name}_salience" />
0
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180 </outputs>
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181 <tests>
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182 <!-- test #1 -->
0
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183 <test>
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184 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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185 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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186 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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187 <param name="tesC" value="kruskal"/>
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188 <param name="facC" value="k10"/>
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189 <param name="pairSigFeatOnly" value="FALSE"/>
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190 <param name="labelFeatures" value="3"/>
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191 <param name="fdr_features" value="250"/>
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192 <param name="levCSV" value="k[12],k[3-4]"/>
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193 <param name="matchingC" value="regex"/>
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194 <output name="contrast_corcov">
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195 <assert_contents>
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196 <!-- column-labels line -->
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197 <has_text text="featureID" />
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198 <has_text text="factorLevel1" />
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199 <has_text text="factorLevel2" />
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200 <has_text text="correlation" />
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201 <has_text text="covariance" />
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202 <has_text text="vip4p" />
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203 <has_text text="vip4o" />
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204 <has_text text="level1Level2Sig" />
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205 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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206 <has_text text="M349.2383T700" />
13
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207 <has_text text="-0.49037231902" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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208 <has_text text="-2111932280.94" />
7
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209 <has_text text="0.4914638" />
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210 <has_text text="0.01302117" />
13
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211 <has_text text="-0.049216260" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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212 <has_text text="-0.00152098716" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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213 <has_text text="2.0603074801" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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214 <has_text text="-0.60020597" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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215 <has_text text="-0.3623876130" />
0
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216 <!-- second matched line -->
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217 <has_text text="M207.9308T206" />
12
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218 <has_text text="0.504885262" />
13
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219 <has_text text="293403792" />
6
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220 <has_text text="0.207196379" />
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221 <has_text text="0.04438632" />
13
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222 <has_text text="0.020749097" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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223 <has_text text="0.005184709" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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224 <has_text text="1.47082346" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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225 <has_text text="2.24325407" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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226 <has_text text="0.38157919" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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227 <has_text text="0.610536188" />
0
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228 </assert_contents>
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229 </output>
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230 <output name="contrast_salience">
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231 <assert_contents>
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232 <!-- column-labels line -->
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233 <has_text text="featureID" />
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234 <has_text text="salientLevel" />
13
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235 <has_text text="salienceRCV" />
0
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236 <has_text text="salience" />
13
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237 <!-- first three matched lines -->
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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238 <has_text text="M207.0654T373" /><has_text text="k4" /><has_text text="0.822733190" /><has_text text="134.087771" /><has_text text="3.9994434" /><has_text text="207.0654" /><has_text text="373" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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239 <has_text text="M222.9585T226" /><has_text text="k2" /><has_text text="0.761200229" /><has_text text="87.3672719" /><has_text text="3.9995358" /><has_text text="222.9585" /><has_text text="226" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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240 <has_text text="M235.0975T362" /><has_text text="k4" /><has_text text="0.209363850" /><has_text text="77.6255643" /><has_text text="3.99606600" /><has_text text="235.0975" /><has_text text="362" />
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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241 </assert_contents>
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242 </output>
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243 </test>
6
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244 <!-- test #2 -->
0
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245 <test>
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246 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
247 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
248 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
249 <param name="tesC" value="kruskal"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
250 <param name="facC" value="k10"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
251 <param name="pairSigFeatOnly" value="TRUE"/>
2
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diff changeset
252 <param name="labelFeatures" value="3"/>
13
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diff changeset
253 <param name="fdr_features" value="ALL"/>
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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254 <param name="levCSV" value="k[12],k[3-4]"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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255 <param name="matchingC" value="regex"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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256 <output name="contrast_corcov">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
257 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
258 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
259 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
260 <has_text text="factorLevel1" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
261 <has_text text="factorLevel2" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
262 <has_text text="correlation" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
263 <has_text text="covariance" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
264 <has_text text="vip4p" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
265 <has_text text="vip4o" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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266 <has_text text="level1Level2Sig" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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267 <!-- first matched line -->
6
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diff changeset
268 <has_text text="M200.005T296" />
13
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parents: 12
diff changeset
269 <has_text text="0.0050579682" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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270 <has_text text="2607493" />
6
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diff changeset
271 <has_text text="0.1157346" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
272 <has_text text="0.0647860" />
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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273 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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274 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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275 <output name="contrast_salience">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
276 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
277 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
278 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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279 <has_text text="salientLevel" />
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
280 <has_text text="salienceRCV" />
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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281 <has_text text="salience" />
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
282 <!-- first three matched lines -->
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
283 <has_text text="M207.0654T373" /><has_text text="k4" /><has_text text="0.822733190" /><has_text text="134.087771" /><has_text text="3.9994434" /><has_text text="207.0654" /><has_text text="373" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
284 <has_text text="M222.9585T226" /><has_text text="k2" /><has_text text="0.761200229" /><has_text text="87.3672719" /><has_text text="3.9995358" /><has_text text="222.9585" /><has_text text="226" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
285 <has_text text="M235.0975T362" /><has_text text="k4" /><has_text text="0.209363850" /><has_text text="77.6255643" /><has_text text="3.99606600" /><has_text text="235.0975" /><has_text text="362" />
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
286 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
287 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
288 </test>
6
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diff changeset
289 <!-- test #3 -->
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
290 <test>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
291 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
292 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
293 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
294 <param name="tesC" value="none"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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295 <param name="facC" value="k10"/>
2
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parents: 1
diff changeset
296 <param name="labelFeatures" value="3"/>
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
297 <param name="fdr_features" value="ALL"/>
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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298 <param name="levCSV" value="k[12],k[3-4]"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
299 <param name="matchingC" value="regex"/>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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300 <output name="contrast_corcov">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
301 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
302 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
303 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
304 <has_text text="factorLevel1" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
305 <has_text text="factorLevel2" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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306 <has_text text="correlation" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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307 <has_text text="covariance" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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308 <has_text text="vip4p" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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309 <has_text text="vip4o" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
310 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
311 <has_text text="M349.2383T700" />
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
312 <has_text text="-0.499225" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
313 <has_text text="-2135165209" />
6
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parents: 5
diff changeset
314 <has_text text="0.5246766" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
315 <has_text text="0.0103341" />
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
316 <!-- second matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
317 <has_text text="M207.9308T206" />
12
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
318 <has_text text="0.4927151212" />
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
319 <has_text text="284608538" />
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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parents: 5
diff changeset
320 <has_text text="0.2111623" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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diff changeset
321 <has_text text="0.0488654" />
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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322 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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323 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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324 <output name="contrast_salience">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
325 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
326 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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327 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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328 <has_text text="salientLevel" />
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
329 <has_text text="salienceRCV" />
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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330 <has_text text="salience" />
13
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331 <!-- first three matched lines -->
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332 <has_text text="M207.0654T373" /><has_text text="k4" /><has_text text="0.822733190" /><has_text text="134.087771" /><has_text text="3.9994434" /><has_text text="207.0654" /><has_text text="373" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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333 <has_text text="M222.9585T226" /><has_text text="k2" /><has_text text="0.761200229" /><has_text text="87.3672719" /><has_text text="3.9995358" /><has_text text="222.9585" /><has_text text="226" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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334 <has_text text="M235.0975T362" /><has_text text="k4" /><has_text text="0.209363850" /><has_text text="77.6255643" /><has_text text="3.99606600" /><has_text text="235.0975" /><has_text text="362" />
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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335 </assert_contents>
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336 </output>
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337 </test>
6
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338 <!-- test #4 -->
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339 <test>
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340 <param name="dataMatrix_in" value="issue1_input_dataMatrix.tsv"/>
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341 <param name="sampleMetadata_in" value="issue1_input_sampleMetadata.tsv"/>
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342 <param name="variableMetadata_in" value="issue1_input_variableMetadata.tsv"/>
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343 <param name="tesC" value="none"/>
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344 <param name="facC" value="tissue_flowering"/>
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345 <param name="labelFeatures" value="3"/>
13
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346 <param name="fdr_features" value="ALL"/>
6
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347 <param name="levCSV" value="*"/>
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348 <param name="matchingC" value="wildcard"/>
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349 <output name="contrast_corcov">
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350 <assert_contents>
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351 <!-- column-labels line -->
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352 <has_text text="featureID" />
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353 <has_text text="factorLevel1" />
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354 <has_text text="factorLevel2" />
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355 <has_text text="correlation" />
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356 <has_text text="covariance" />
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357 <has_text text="vip4p" />
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358 <has_text text="vip4o" />
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359 <!-- first matched line -->
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360 <has_text text="NM516T251" />
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361 <has_text text="flower_yes" />
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362 <has_text text="other" />
12
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diff changeset
363 <has_text text="0.3499550705" />
13
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364 <has_text text="11.609255" />
7
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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365 <has_text text="0.43664386" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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366 <has_text text="0.587701897" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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367 <has_text text="0.026082688" />
066b1f409e9f planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e73fabe1b3c871abbcb2e89914c181149c8e2066
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368 <has_text text="0.0437742145" />
6
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369 <has_text text="516.0845" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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370 <has_text text="250.8762" />
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371 </assert_contents>
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372 </output>
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373 <output name="contrast_salience">
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374 <assert_contents>
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375 <!-- column-labels line -->
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376 <has_text text="featureID" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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377 <has_text text="salientLevel" />
13
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378 <has_text text="salienceRCV" />
6
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379 <has_text text="salience" />
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380 <has_text text="mz" />
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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381 <has_text text="rt" />
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382 <!-- first matched line -->
13
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diff changeset
383 <has_text text="NM517T428" /><has_text text="flower_yes" /><has_text text="0.02765631" /><has_text text="7.8343993" /><has_text text="1.27813793" /><has_text text="517.121714" /><has_text text="428.306854248" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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384 <has_text text="NM517T426_1" /><has_text text="0.0290065" /><has_text text="7.7151305" /><has_text text="1.2758886" /><has_text text="517.09367125" /><has_text text="426.233886719" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
385 <has_text text="NM516T284_2" /><has_text text="0.022883902" /><has_text text="7.6379724" /><has_text text="1.25603610" /><has_text text="516.082005177" /><has_text text="283.569198608" />
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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386 </assert_contents>
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387 </output>
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388 </test>
10
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389 <!-- test #5 -->
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390 <test>
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391 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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392 <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
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393 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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394 <param name="tesC" value="none"/>
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552
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395 <param name="facC" value="k._10"/>
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396 <param name="labelFeatures" value="3"/>
13
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397 <param name="fdr_features" value="ALL"/>
10
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diff changeset
398 <param name="levCSV" value="k1,k.2"/>
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399 <param name="matchingC" value="none"/>
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400 <output name="contrast_corcov">
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diff changeset
401 <assert_contents>
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402 <!-- column-labels line -->
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403 <has_text text="featureID" />
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404 <has_text text="factorLevel1" />
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405 <has_text text="factorLevel2" />
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406 <has_text text="correlation" />
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407 <has_text text="covariance" />
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diff changeset
408 <has_text text="vip4p" />
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409 <has_text text="vip4o" />
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552
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diff changeset
410 <!-- first matched line -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552
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diff changeset
411 <has_text text="M349.2383T700" />
12
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diff changeset
412 <has_text text="0.61594030" />
13
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413 <has_text text="3489481837.9" />
11
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414 <has_text text="0.54672558" />
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415 <has_text text="0.3920409" />
10
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416 <!-- second matched line -->
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417 <has_text text="M207.9308T206" />
12
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418 <has_text text="-0.89716403" />
13
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419 <has_text text="-585563327.7" />
11
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420 <has_text text="0.270297" />
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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421 <has_text text="0.037661" />
10
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422 </assert_contents>
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423 </output>
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424 </test>
11
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425 <!-- test #6 - issue 6 -->
10
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426 <test>
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427 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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428 <param name="sampleMetadata_in" value="issue6_input_sampleMetadata.tsv"/>
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429 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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430 <param name="tesC" value="none"/>
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431 <param name="facC" value="k._10"/>
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432 <param name="labelFeatures" value="3"/>
13
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433 <param name="fdr_features" value="ALL"/>
10
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434 <param name="levCSV" value="k_3,k-4"/>
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435 <param name="matchingC" value="none"/>
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436 <output name="contrast_corcov">
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437 <assert_contents>
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438 <!-- column-labels line -->
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439 <has_text text="featureID" />
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440 <has_text text="factorLevel1" />
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441 <has_text text="factorLevel2" />
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442 <has_text text="correlation" />
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443 <has_text text="covariance" />
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444 <has_text text="vip4p" />
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445 <has_text text="vip4o" />
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446 <!-- first matched line -->
9a52306991b3 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 5aeb583ae4a55cc24289f9d95590e02553a89552
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447 <has_text text="M349.2383T700" />
13
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448 <has_text text="-0.1221966" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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449 <has_text text="-917311734" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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450 <has_text text="0.0304592" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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451 <has_text text="0.104748883" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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452 <has_text text="-0.002736415" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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453 <has_text text="-0.0113968" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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454 <has_text text="0.387723" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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455 <has_text text="-0.3812168081" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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456 <has_text text="0.154611878" />
10
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457 </assert_contents>
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458 </output>
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459 </test>
12
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diff changeset
460 <!-- test #7 - issue 8 -->
11
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461 <test>
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462 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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463 <param name="sampleMetadata_in" value="issue8_input_sampleMetadata.tsv"/>
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464 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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465 <param name="tesC" value="none"/>
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466 <param name="facC" value="k._10"/>
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467 <param name="labelFeatures" value="3"/>
13
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468 <param name="fdr_features" value="ALL"/>
11
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469 <param name="levCSV" value="k_3,k-4"/>
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470 <param name="matchingC" value="none"/>
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471 <output name="contrast_corcov">
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472 <assert_contents>
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473 <!-- column-labels line -->
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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474 <has_text text="featureID" />
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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475 <has_text text="factorLevel1" />
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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476 <has_text text="factorLevel2" />
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477 <has_text text="correlation" />
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478 <has_text text="covariance" />
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479 <has_text text="vip4p" />
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480 <has_text text="vip4o" />
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481 <!-- k1 rejected by levCSV, leaving only k_3 and k-4 -->
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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482 <not_has_text text="k1" />
ddcc33ff3205 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 4428e3252d54c8a8e0e5d85e8eaaeb13e9b21de7
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483 <not_has_text text="other" />
13
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484 <!-- first matched line -->
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485 <has_text text="M200.005T296" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
486 <has_text text="-0.1829149760" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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487 <has_text text="-115723402" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
488 <has_text text="0.0892595" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
489 <has_text text="0.00492288" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
490 <has_text text="-0.00801895" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
491 <has_text text="0.0005356178" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
492 <has_text text="0.1848186" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
493 <has_text text="-0.428802311" />
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
494 <has_text text="0.0882045811" />
11
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495 </assert_contents>
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496 </output>
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497 </test>
0
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498 </tests>
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499 <help><![CDATA[
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500
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501 **Run OPLS-DA Contrasts of Univariate Results**
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502 -----------------------------------------------
0
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503
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504 **Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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505
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506 **Release Notes** - https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper#release-notes
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507
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508 Motivation
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509 ----------
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510
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511 OPLS-DA and the SIMCA S-PLOT (Wiklund *et al.*, 2008) may be employed to draw attention to metabolomic features that are potential biomarkers, i.e. features that are potentially useful when assigning a sample to one of two classes (e.g. Sun *et al.*, 2016). Workflow4Metabolomics (W4M, Giacomoni *et al.*, 2014, Guitton *et al.*, 2017) provides a suite of tools for preprocessing and statistical analysis of LC-MS, GC-MS, and NMR metabolomics data; however, it does not (as of release 3.2) include a tool for making the equivalent of an S-PLOT.
0
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512
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513 The S-PLOT is computed from mean-centered, pareto-scaled data. This plot presents the correlation of the first score vector from an OPLS-DA model with the sample-variables used to produce that model versus the covariance of the scores with the sample-variables. For OPLS-DA, the first score vector represents the variation among the sample-variables that is related to the predictor (i.e., the contrasting factor); the second score vector, variation that is orthogonal to the predictor.
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514
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515 The primary aims of this tool are:
0
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516
1
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517 - To compute and visualize multiple contrasts with OPLS-DA and the covariance vs. correlation plot.
0
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518 - To write the results to data files for use in further multivariate analysis or visualization.
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519
1
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520 Note: This tool only supports categorical factors with non-numeric level-names.
0
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521
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522 Description
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523 -----------
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524
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525 The purpose of the 'OPLS-DA Contrasts' tool is to visualize GC-MS or LC-MS features that are possible biomarkers.
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526
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527 The W4M 'Univariate' tool (Th]]>&#233;<![CDATA[venot *et al.*, 2015) adds the results of family-wise corrected pairwise significance-tests as columns of the **variableMetadata** dataset.
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528 For instance, if Kruskal-Wallis testing were perfomred on a column named 'cluster' in sampleMetadata that has values 'k1' and 'k2' and at least one other value:
0
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529
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530 - A column of variableMetadata would be labelled 'cluster_kruskal_sig' and would have values '1' and '0'; when the samples are grouped by 'cluster', '1' means that there is strong evidence against the hypothesis that there is no difference among the intensities for the feature across all sample-groups.
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531 - A column of variableMetadata would be labelled 'cluster_kruskal_k1.k2_sig' and would have values '1' and '0', where '1' means that there is significant evidence against the hypothesis that samples from sampleMetadata whose 'cluster' column contains 'k1' or 'k2' have the same intensity for that feature.
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532
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533 The 'OPLS-DA Contrasts' tool produces graphics and data for OPLS-DA contrasts of feature-intensities between significantly different pairs of factor-levels. For each factor-level, the tool performs a contrast with all other factor-levels combined and then separately with each other factor-level.
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534
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535 **Along the left-to-right axis, the plots show the supervised projection of the variation explained by the predictor** (i.e., the factor specified when invoking the tool); **the top-to-bottom axis displays the variation that is orthogonal to the predictor level** (i.e., independent of it).
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536
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537 Although this tool can be used in a purely exploratory manner by supplying the variableMetadata file without the columns added by the W4M 'Univariate' tool, **a preferable workflow may be to use univariate testing to exclude features that are not significantly different and then to use OPLS-DA to visualize the differences identified in univariate testing** (Th]]>&#233;<![CDATA[venot *et al.*, 2015); an appropriate exception would be to visualize contrasts of a specific list of metabolites. If you do exclude features, however, make sure that you set the advanced parameter "How many features for p-value calculation?" accordingly.
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538
2
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539 It must be stressed that there may be no *single* definitive computational approach to select features that are reliable biomarkers, especially from a small number of samples or experiments. A few possible choices are:
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540
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541 - picking features with maximum loadings along the projection parallel to the predictor (loadp),
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542 - examining extreme values on S-PLOTs
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543 - examining "variable importance in projection VIP for OPLS-DA" (Galindo-Prieto *et al.* 2014), and
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544 - examining a feature's "selectivity ratio" (Rajalahti *et al.*, 2009).
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545
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546 In this spirit, this tool reports the S-PLOT covariance and correlation (Wiklund *op. cit.*) and VIP metrics, and it introduces an informal "salience" metric to flag features that may merit attention without dimensional reduction; future versions may add selectivity ratio.
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547
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548 For a more systematic approach to biomarker identification, please consider the W4M 'biosigner' tool (Rinuardo *et al.* 2016), which applies three different identification metrics to the selection process. Regardless of how any potential biomarker is identified, further validation analysis (e.g., independent confirmatory experiments) is needed before it can be recommended for general application.
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549
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550
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551 W4M Workflow Position
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552 ---------------------
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553
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554 - Upstream tool: **Univariate** (category: Statistical Analysis) or any **Preprocessing** tool that produces or updates a 'variableMetadata' file.
0
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555 - Downstream tool categories: **Statistical Analysis**
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556
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557 Input files
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558 -----------
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559
1
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560 +----------------------+-----------+
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561 | File | Format |
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562 +======================+===========+
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563 | Data matrix | tabular |
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564 +----------------------+-----------+
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565 | Sample metadata | tabular |
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566 +----------------------+-----------+
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567 | Variable metadata | tabular |
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568 +----------------------+-----------+
0
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569
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570 Output files
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571 ------------
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572
1
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573 +-------------------------------------------+-----------+
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574 | File | Format |
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575 +===========================================+===========+
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576 | Contrast detail | pdf |
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577 +-------------------------------------------+-----------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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578 | Contrast "corrlation and covariance" data | tabular |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
579 +-------------------------------------------+-----------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
580 | Feature "salience" data | tabular |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
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581 +-------------------------------------------+-----------+
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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582
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
583 Parameters
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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584 ----------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
585
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
586 [IN] Data matrix file
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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587 | variable x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with '.' as decimal, and 'NA' for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
588 |
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
589
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
590 [IN] Sample metadata file
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
591 | sample x metadata **sampleMetadata** (tabular separated values) file of the numeric and/or character sample metadata, with '.' as decimal and 'NA' for missing values
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
592 |
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
593
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
594 [IN] Variable metadata file
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
595 | variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with '.' as decimal and 'NA' for missing values
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
596 |
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
597
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
598 [IN] Test
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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599 | Name of the **statistical test** - a component of column names in variable metadata table
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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600 | May be one of 'none', 'ttest', 'gwilcoxon', 'anova', 'kruskal', 'pearson', 'spearman'
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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601 |
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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602
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
603 [IN] Factor of interest
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
604 | Name of the **column of sampleMetadata** corresponding to the qualitative or quantitative variable
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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605 |
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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606
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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607 [IN] Retain only pairwise-significant features
5
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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608 | *Note that when 'Test' is 'none', all features are included in the analysis and this parameter is not settable.*
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
609 | When **true**, for each contrast of two levels, include only those features which pass the significance threshold for that contrast. Choosing true results in an OPLS-DA model that better reflects and visualizes the difference detected by univariate analysis, with somewhat increased reliability of prediction (as assessed by cross-validation).
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
610 | When **false**, include all features that pass the significance threshold when testing for difference across all factor-levels. This choice produces a plot that displays more features but is not necessarily more informative.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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611 |
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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612
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
613 [IN] Levels of interest
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
614 | Comma-separated **level-names** (or comma-less regular expressions to match level-names) to consider in analysis; must match at least two levels; may include wild cards or regular expressions.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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615 |
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
616
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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617 [IN] Level-name matching
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
618 | Indicator of **how levels are to be specified generically** (if at all) - wild cards, regular expressions, or none (no generic matching).
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
619 |
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
620
2
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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parents: 1
diff changeset
621 [IN] Label how many extreme features
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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622 | Specify the number of features at each of the loading-extremes that should be labelled (with the name of the feature) on the covariance-vs.-correlation plot; specify 'ALL' to label all features; this choice has no effect on the OPLS-DA loadings plot.
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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diff changeset
623 |
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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diff changeset
624
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
625 [IN] (Advanced) C-plot Y-axis
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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626 | Choose whether C-plots should plot the correlation (the default) or the covariance *vs.* VIP.
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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627 |
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
628
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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629 [IN] (Advanced) Produce predictor C-plot
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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630 | Choose whether a C-plot should be produced for the projections parallel to the predictor.
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
631 |
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
632
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
633 [IN] (Advanced) Produce orthogonal C-plot
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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634 | Choose whether a C-plot should be produced for the projections orthogonal to the predictor.
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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635 |
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
636
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
637 [IN] (Advanced) How many features for p-value calculation?
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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638 | You will need to use this option when statistical criteria have previously been applied to remove features in the data matrix. This is important for adjusting the p-values for correlation of the scores with each feature; this adjustment is necessary to avoid underestimation of the p-values. If this is applicable, specify the sum of the number of features removed and the number of features in the data matrix.
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
639 |
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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diff changeset
640
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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641 [OUT] Contrast-detail output PDF
12
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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642 | File containing several plots for each two-projection OPLS-DA analysis.
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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diff changeset
643
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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644 - (first row, left) **correlation-versus-covariance plot** of OPLS-DA results
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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645
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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646 - This is a work-alike for the S-PLOT described in Wiklund, (*op. cit.*), ignoring samples with missing values;
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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647 - point-color becomes saturated as the "variable importance in projection to the predictive components" (VIP\ :subscript:`4,p` from Galindo-Prieto *op. cit.*) ranges from 0.83 and 1.21 (Mehmood *et al.* 2012), for use to identify features for consideration as biomarkers;
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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648 - plot symbols are diamonds when the p-value of the correlation, adjusted for family-wise error rate (Yekutieli *et al.*, 2001), is greater than 0.05, circles when it is less than 0.01, and triangles when between 0.01 and 0.05.
6
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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649 - (second row, left) **model-overview plot** for the two projections; grey bars are the correlation coefficient for the fitted data; black bars indicate performance in cross-validation tests (Th]]>&#233;<![CDATA[venot, 2017)
7bd523ca1f9a planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit cafda5095a79ce2376325b57337302f95137195d
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650 - (first row, right) OPLS-DA **scores-plot** for the two projections (Th]]>&#233;<![CDATA[venot *et al.*, 2015)
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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651 - (second row, right) **correlation-versus-covariance plot** of OPLS-DA results **orthogonal to the predictor** (see section "S-Plot of Orthogonal Component" in Wiklund, *op. cit.*, pp. 120-121; this characterizes variation of features that is *independent of the predictor*).
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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652 - (third row, left, when "**predictor C-plot**" is chosen under "Advanced") plot of the correlation (or covariance) vs. the VIP\ :subscript:`4,p` (Galindo-Prieto *op. cit.*), to assist in identifying features for consideration as biomarkers.
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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653 - (third row, right, when "**orthogonal C-plot**" is chosen under "Advanced") plot of the correlation (or covariance) vs. the VIP\ :subscript:`4,o` (*ibid.*), to assist in identifying features varying considerably without regard to the predictor.
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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654
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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655 [OUT] Contrast Correlation-Covarinace data TABULAR
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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656 | A tab-separated values file of metadata for each feature for each contrast in which it was included.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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657 | Thus, a given feature may appear many times, but *the combination of featureID, factorLevel1, and factorLevel2 will be unique.*
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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658 | This file has the following columns:
0
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659
13
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660 - **featureID** - feature identifier
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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661 - **factorLevel1** - factor-level 1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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662 - **factorLevel2** - factor-level 2 (or "other" when contrasting factor-level 1 with all other levels)
13
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663 - **correlation**\ (t\ :subscript:`p`,X\ :subscript:`i`) - for this feature (i), correlation of sample intensities for this feature (X\ :subscript:`i`) with the OPLS-DA projection's first set of scores (t\ :subscript:`p`, i.e., the scores explaining the difference between the features), computed (omitting samples missing values) using the R *stats::cor* function with the 'pearson' method (R Core Team, 2018); this is negative when intensity for level 1 is greater than for level 2
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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664 - **covariance**\ (t\ :subscript:`p`,X\ :subscript:`i`) - computed as for correlation but using the R *stats::cov* function (*ibid.*) in lieu of *stats::cor*; this is also negative when intensity for level 1 is greater than for level 2
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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665 - **vip4p** - "variable importance in projection" to the predictive projection, VIP\ :subscript:`4,p` (Galindo-Prieto *op. cit.*)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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666 - **vip4o** - "variable importance in projection" to the orthogonal projection, VIP\ :subscript:`4,o` (*ibid.*)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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667 - **loadp** - variable loading for the predictive projection (Wiklund *op. cit.*)
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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668 - **loado** - variable loading for the orthogonal projection (*ibid.*)
12
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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669 - **cor_p_val_raw** - p-value for Fisher-transformed correlation (Fisher, 1921; Snedecor, 1980; see also https://en.wikipedia.org/wiki/Fisher_transformation), with no family-wise error-rate correction.
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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670 - **cor_p_value** - p-value for Fisher-transformed correlation, adjusted for family-wise error rate (Yekutieli *et al.*, 2001).
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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671 - **cor_ci_lower** - lower limit of 95% confidence interval for correlation, based on cor_p_value
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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672 - **cor_ci_upper** - upper limit of 95% confidence interval for correlation, based on cor_p_value
12
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673 - **mz** - *m/z* ratio for feature, copied from input variableMetadata
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674 - **rt** - retention time for feature, copied from input variableMetadata
13
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675 - **level1Level2Sig** (Only present when a test other than "none" is chosen) - '1' when feature varies significantly across all classes (i.e., not pair-wise); '0' otherwise
0
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676
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677 [OUT] Feature "Salience" data TABULAR
6
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678 | Metrics for the "salient level" for each feature, i.e., the level at which the feature is more prominent than any other level. This is *not* at all related to the SIMCA OPLS-DA S-PLOT; rather, it is intended as a potential way to discover features for consideration as potential biomarkers without dimensionally reducting the data. This is a tab-separated values file having the following columns:
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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679
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680 - **featureID** - feature identifier
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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681 - **salientLevel** - salient level, i.e., for the feature, the class-level having the greatest median intensity
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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682 - **salienceRCV** - salience robust coefficient of variation, i.e., for the feature, the mean absolute deviation of the intensity for the salient level divided by the median intensity for the salient level
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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683 - **relativeSalientDistance** - relative salient distance, i.e., for the feature, the distance between the two highest class-level medians divided by the square root of the mean absolute deviations of those two class-level's intensities
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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684 - **salience** - salience, i.e., for the feature, the median of the class-level having the greatest intensity divided by the mean of the medians for all class-levels
13
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685 - **mz** - *m/z* ratio for feature, copied from input variableMetadata
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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686 - **rt** - retention time for feature, copied from input variableMetadata
0
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687
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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688 Wild card patterns to match level-names
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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689 ---------------------------------------
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690
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691 "wild card" patterns may be used to select level-names.
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692
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693 - use '``?``' to match a single character
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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694 - use '``*``' to match zero or more characters
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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695 - the entire pattern must match the level name
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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696
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697 For example
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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698
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699 - '``??.le*``' matches '``my.level``' but not '``my.own.level``'
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700 - '``*.level``' matches '``my.level``' and '``my.own.level``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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701 - '``*.level``' matches neither '``my.level``' nor '``my.own.level``'
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702
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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703 Regular expression patterns to match level-names
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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704 ------------------------------------------------
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705
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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706 "regular expression" patterns may be used to select level-names.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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707
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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708 POSIX 1003.2 standard regular expressions allow precise pattern-matching and are exhaustively defined at:
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709 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
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710
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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711 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
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712
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713 - '``^``' matches the beginning of a level-name
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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714 - '``$``' matches the end of a level-name
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715 - '``.``' outside of square brackets matches a single character
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716 - '``*``' matches character specified immediately before zero or more times
1
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717 - Square brackets specify a set of characters to be matched. Within square brackets:
0
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718
1
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719 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
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720 - '``-``' is used to specify ranges of characters
0
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721
1
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722 Caveat: The tool wrapper uses the comma ('``,``') to split a list of sample-level names, so **commas may not be used within regular expressions for this tool.**
0
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723
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724 First Example: Consider a field of level-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
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725
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726 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-levels as '``front3,front6,front9,front12``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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727 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-levels as '``front3,marq3``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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728 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-levels as '``front12,marq12``'
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729 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-levels as '``front3,front6,front9,marq3,marq6,marq9``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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730
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731 Second Example: Consider these regular expression patterns as possible matches to a sample-level name '``AB0123``':
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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732
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
733 - '``^[A-Z][A-Z][0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
734 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
735 - '``^[A-Z][0-9]*``' - MATCHES '``**^A** B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
736 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
737 - '``^[A-Z][A-Z]*[0-9][0-9]$``' - NO MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
738 - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
739
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
740 Working examples
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
741 ----------------
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
742
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
743 **Input files**
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
744
9
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
745 +-----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
746 | Download from URL |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
747 +===============================================================================================================================================+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
748 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/input_dataMatrix.tsv |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
749 +-----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
750 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/input_sampleMetadata.tsv |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
751 +-----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
752 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/input_variableMetadata.tsv |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
753 +-----------------------------------------------------------------------------------------------------------------------------------------------+
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
754
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
755 **Example 1:** Include in the analysis only features identified as pair-wise significant in the Univariate test.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
756
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
757 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
758 | Input Parameter or Result | Value |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
759 +============================================+========================================================================================================================================+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
760 | Factor of interest | k10 |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
761 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
762 | Univariate Significance-Test | kruskal |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
763 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
764 | Retain only pairwise-significant features | Yes |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
765 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
766 | Levels of interest | k[12],k[3-4] |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
767 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
768 | Level-name matching | use regular expressions for matching level-names |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
769 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
770 | Number of features having extreme loadings | ALL |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
771 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
eschen42
parents: 12
diff changeset
772 | How many features for p-value calculation? | 250 |
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
eschen42
parents: 12
diff changeset
773 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
9
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
774 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov.tsv |
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
775 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
9
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
776 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience.tsv |
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
777 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
9
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
778 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail.pdf |
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
779 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
780
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
781 **Example 2:** Include in the analysis only features identified as overall-significant in the Univariate test. Note that this even includes these features in contrasts where they were not determined to be pair-wise significant in the Univariate test. Thus, more features are included than in Example 1.
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
782
9
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
783 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
784 | Input Parameter or Result | Value |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
785 +============================================+============================================================================================================================================+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
786 | Factor of interest | k10 |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
787 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
788 | Univariate Significance-Test | kruskal |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
789 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
790 | Retain only pairwise-significant features | No |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
791 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
792 | Levels of interest | ``*`` |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
793 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
794 | Level-name matching | use wild cards for matching level-names |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
795 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
796 | Number of features having extreme loadings | 5 |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
797 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
eschen42
parents: 12
diff changeset
798 | How many features for p-value calculation? | ALL |
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
eschen42
parents: 12
diff changeset
799 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
9
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
800 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov_all.tsv |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
801 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
802 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience_all.tsv |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
803 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
804 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail_all.pdf |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
805 +--------------------------------------------+--------------------------------------------------------------------------------------------------------------------------------------------+
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
806
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
807 **Example 3:** Include all features in the analysis without regard to Univariate testing. Univariate testing is not even a pre-requisite to using the tool when 'none' is selected for the test. Thus, more features are included than in Example 2.
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
808
9
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
809 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
810 | Input Parameter or Result | Value |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
811 +============================================+==============================================================================================================================================+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
812 | Factor of interest | k10 |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
813 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
814 | Univariate Significance-Test | none |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
815 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
816 | Levels of interest | k[12],k[3-4] |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
817 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
818 | Level-name matching | use regular expressions for matching level-names |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
819 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
820 | Number of features having extreme loadings | 0 |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
821 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
eschen42
parents: 12
diff changeset
822 | How many features for p-value calculation? | ALL |
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
eschen42
parents: 12
diff changeset
823 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
9
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
824 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov_global.tsv |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
825 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
826 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience_global.tsv |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
827 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
828 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail_global.pdf |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
829 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
830
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
831 **Example 4:** Analysis of a two-level factor (including all features). This suppresses the contrasts of "each factor vs. the aggregate of all the others".
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
832
9
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
833 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
834 | Input Parameter or Result | Value |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
835 +============================================+==============================================================================================================================================+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
836 | Factor of interest | lohi |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
837 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
838 | Univariate Significance-Test | none |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
839 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
840 | Levels of interest | low,high |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
841 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
842 | Level-name matching | use regular expressions for matching level-names |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
843 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
844 | Number of features having extreme loadings | 3 |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
845 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
eschen42
parents: 12
diff changeset
846 | How many features for p-value calculation? | ALL |
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
eschen42
parents: 12
diff changeset
847 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
9
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
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parents: 8
diff changeset
848 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_corcov_lohi.tsv |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
849 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
850 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_salience_lohi.tsv |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
851 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
852 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/tools/w4mcorcov/test-data/expected_contrast_detail_lohi.pdf |
06c51af11531 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit fda7ea61f0a082fd0c28730e471e66c92aaa04d0
eschen42
parents: 8
diff changeset
853 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------------+
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
854
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
855
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
856 Trademarks
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
857 ----------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
858
4
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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parents: 3
diff changeset
859 OPLS-DA, SIMCA, and S-PLOT are registered trademarks of the Umetrics company. http://umetrics.com/about-us/trademarks
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
860
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
861
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
862 ]]></help>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
863 <citations>
5
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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parents: 4
diff changeset
864 <!-- this tool -->
2
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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parents: 1
diff changeset
865 <citation type="doi">10.5281/zenodo.1034784</citation>
13
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
866 <!-- R project -->
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
867 <citation type="bibtex"><![CDATA[
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
868 @Manual{,
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
869 title = {R: A Language and Environment for Statistical Computing},
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
870 author = {{R Core Team}},
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
871 organization = {R Foundation for Statistical Computing},
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
872 address = {Vienna, Austria},
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
873 year = {2018},
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
874 url = {https://www.R-project.org/},
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
875 }
2ae2d26e3270 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit e89c652c0849eb1d5a1e6c9100c72c64a8d388b4
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parents: 12
diff changeset
876 ]]></citation>
12
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
877 <!-- Fisher_1921: Fisher z-transformation of correlation coefficient -->
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
878 <citation type="bibtex"><![CDATA[
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
879 @article{Fisher_1921,
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
880 author = {Fisher, R. A.},
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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diff changeset
881 title = {{On the probable error of a coefficient of correlation deduced from a small sample}},
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
882 journal = {Metron},
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
883 year = {1921},
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
884 volume = {1},
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
885 pages = {3--32},
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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diff changeset
886 note = {Defines the Fisher z-transformation of a coefficient of correlation. Citation adapted from http://www.citeulike.org/group/894/article/2344770},
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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diff changeset
887 url = {https://digital.library.adelaide.edu.au/dspace/bitstream/2440/15169/1/14.pdf},
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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diff changeset
888 }
ddaf84e15d06 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 6775c83b89d9d903c81a2229cdc200fc93538dfe-dirty
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parents: 11
diff changeset
889 ]]></citation>
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
890 <!-- Galindo_Prieto_2014 Variable influence on projection (VIP) for OPLS -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
891 <citation type="doi">10.1002/cem.2627</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
892 <!-- Giacomoni_2014 W4M 2.5 -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
893 <citation type="doi">10.1093/bioinformatics/btu813</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
894 <!-- Guitton_2017 W4M 3.0 -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
895 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
896 <!-- Mehmood_2012 PLS-based variable-selection -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
897 <citation type="doi">10.1186/1748-7188-6-27</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
898 <!-- Rajalahti_2009 Biomarker discovery using selectivity ratio -->
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899 <citation type="doi">10.1016/j.chemolab.2008.08.004</citation>
1
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900 <!-- Rinuardo 2016 -->
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901 <citation type="doi">10.3389/fmolb.2016.00026</citation>
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902 <!-- Sun_2016 Urinary Biomarkers for adolescent idiopathic scoliosis -->
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903 <citation type="doi">10.1038/srep22274</citation>
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904 <!-- Snedecor_1980: Fisher z-transformation of correlation coefficient -->
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905 <citation type="bibtex"><![CDATA[
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906 @book{Snedecor_1980,
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907 author = {Snedecor, George W. and Cochran, William G.},
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908 title = {Statistical methods},
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909 publisher = {Iowa State University Press},
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910 year = {1980},
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911 pages = {186},
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912 isbn = {0813815606},
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913 language = {eng},
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914 keyword = {Statistics, Statistics as Topic -- methods},
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915 lccn = {80014582},
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916 edition = {7th ed..},
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917 address = {Ames, Iowa},
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918 }
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919 ]]></citation>
4
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920 <!-- Thevenot_2015 Urinary metabolome statistics -->
0
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921 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
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922 <!-- ropls package -->
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923 <citation type="bibtex"><![CDATA[
1
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924 @incollection{Thevenot_ropls_2017,
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925 author = {Th{\'{e}}venot, Etienne A.},
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926 title = {ropls: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data},
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927 publisher = {bioconductor.org},
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928 year = {2017},
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929 doi = {10.18129/B9.bioc.ropls},
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930 booktitle = {Bioconductor: Open source software for bioinformatics},
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931 address = {Roswell Park Cancer Institute},
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932 }
0
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933 ]]></citation>
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934 <!-- Wiklund_2008 OPLS-DA and S-PLOT -->
0
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935 <citation type="doi">10.1021/ac0713510</citation>
12
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936 <!-- Yekutieli_2001 The control of the false discovery rate in multiple testing under dependency -->
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937 <citation type="doi">10.1214/aos/1013699998</citation>
0
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938 </citations>
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939 <!--
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940 vim:et:sw=4:ts=4
0
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941 -->
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942 </tool>