Mercurial > repos > eschen42 > w4mcorcov

annotate w4mcorcov.xml @ 5:50f60f94c034 draft

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planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
author eschen42
date Fri, 30 Mar 2018 14:59:19 -0400
parents 8bba31f628da
children 7bd523ca1f9a
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1 <tool id="w4mcorcov" name="OPLS-DA_Contrasts" version="0.98.8">
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3 <description>OPLS-DA Contrasts of Univariate Results</description>
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4
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5 <macros>
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6 <xml name="paramPairSigFeatOnly">
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7 <param
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8 name="pairSigFeatOnly"
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9 type="boolean"
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10 checked="true"
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11 truevalue="TRUE"
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12 falsevalue="FALSE"
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13 label="Retain only pairwise-significant features"
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14 help="When this option is set to 'Yes', analysis will be performed including only features that differ 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 any feature that is not significantly different across all levels). See examples below." />
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15 </xml>
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16 </macros>
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17
0
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18 <requirements>
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19 <requirement type="package">r-batch</requirement>
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20 <requirement type="package">bioconductor-ropls</requirement>
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21 </requirements>
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23 <stdio>
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24 <exit_code range="1:" level="fatal" />
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25 </stdio>
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26
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27 <command><![CDATA[
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28 cd $__tool_directory__; Rscript w4mcorcov_wrapper.R
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29 dataMatrix_in "$dataMatrix_in"
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30 sampleMetadata_in "$sampleMetadata_in"
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31 variableMetadata_in "$variableMetadata_in"
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32 facC "$facC"
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33 #if str( $signif_test.tesC ) == "none":
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34 tesC "none"
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35 pairSigFeatOnly "FALSE"
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36 #else:
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37 tesC "$signif_test.tesC"
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38 pairSigFeatOnly "$signif_test.pairSigFeatOnly"
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39 #end if
0
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40 levCSV '$levCSV'
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41 matchingC '$matchingC'
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42 labelFeatures '$labelFeatures'
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43 contrast_detail '$contrast_detail'
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44 contrast_corcov '$contrast_corcov'
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45 contrast_salience '$contrast_salience'
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46 ]]></command>
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47
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48 <inputs>
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49 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="Features x samples (tabular data - decimal: '.'; missing: NA; mode: numerical; separator: tab character)" />
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50 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="Samples x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
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51 <param name="variableMetadata_in" label="Variable metadata file (ideally from Univariate)" type="data" format="tabular" help="Features x metadata (tabular data - decimal: '.'; missing: NA; mode: character or numerical; separator: tab character)" />
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52 <param name="facC" label="Factor of interest" type="text" 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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53 <conditional name="signif_test">
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54 <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; that name must also be a portion of the column names in that file.">
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55 <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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56 <option value="ttest">ttest - Student's t-test (parametric test, qualitative factor with exactly 2 levels)</option>
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57 <option value="anova">anova - Analysis of variance (parametric test, qualitative factor with more than 2 levels)</option>
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58 <option value="wilcoxon">wilcoxon - Wilcoxon rank test (nonparametric test, qualitative factor with exactly 2 levels)</option>
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59 <option value="kruskal">kruskal - Kruskal-Wallis rank test (nonparametric test, qualitative factor with more than 2 levels)</option>
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60 </param>
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61 <when value="none" />
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62 <when value="ttest">
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63 <expand macro="paramPairSigFeatOnly" />
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64 </when>
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65 <when value="anova">
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66 <expand macro="paramPairSigFeatOnly" />
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67 </when>
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68 <when value="wilcoxon">
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69 <expand macro="paramPairSigFeatOnly" />
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70 </when>
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71 <when value="kruskal">
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72 <expand macro="paramPairSigFeatOnly" />
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73 </when>
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74 </conditional>
1
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75 <param name="levCSV" label="Levels of interest" type="text" value = "*" help="Comma-separated level-names (or comma-less 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 - 'a,b' is correct, but 'a , b' is not and may fail or give different results.">
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76 <sanitizer>
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77 <valid initial="string.letters">
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78 <add preset="string.digits"/>
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79 <add value="&#36;" /> <!-- $ dollar, dollar-sign -->
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80 <add value="&#40;" /> <!-- ( left-paren -->
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81 <add value="&#41;" /> <!-- ) right-paren -->
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82 <add value="&#42;" /> <!-- * splat, asterisk -->
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83 <add value="&#43;" /> <!-- + plus -->
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84 <add value="&#44;" /> <!-- , comma -->
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85 <add value="&#45;" /> <!-- - dash, minus-sign -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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86 <add value="&#46;" /> <!-- . dot, period -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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87 <add value="&#58;" /> <!-- : colon -->
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88 <add value="&#59;" /> <!-- ; semi, semicolon -->
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89 <add value="&#63;" /> <!-- ? what, question mark -->
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90 <add value="&#91;" /> <!-- [ l-squib, left-squre-bracket -->
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91 <add value="&#92;" /> <!-- \ whack, backslash -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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92 <add value="&#93;" /> <!-- ] r-squib, right-squre-bracket -->
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93 <add value="&#94;" /> <!-- ^ hat, caret -->
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94 <add value="&#123;" /> <!-- { l-cube, left-curly-bracket -->
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95 <add value="&#124;" /> <!-- | pipe -->
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96 <add value="&#125;" /> <!-- } r-cube, right-curly-bracket -->
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97 <!-- 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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98 </valid>
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99 </sanitizer>
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100 </param>
2
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101 <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.)">
1
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102 <option value="none">do no generic matching (default)</option>
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103 <option value="wildcard" selected="true">use wild-cards for matching level-names</option>
0
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104 <option value="regex">use regular expressions for matching level-names</option>
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105 </param>
2
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106 <param name="labelFeatures" type="text" value="3" label="How many features having extreme loadings should be labelled on cov-vs.-cor plot" 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."/>
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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107 </inputs>
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108
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109 <outputs>
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110 <!--
2
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111 pdf1: summaries of each contrasts, clearly labelled by level=pair name
0
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112 * first PCA score-plot
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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113 * then PLS score-plot
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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114 * then PLS S-PLOT; color in red features with VIP > 1; color in grey any non-pairwise-significant features, if these are included
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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115 -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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116 <data name="contrast_detail" label="${tool.name}_${variableMetadata_in.name}_detail" format="pdf" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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117 <!--
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118 tsv1: cor and cov table with columns:
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119 * feature-ID
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120 * factor-level 1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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121 * factor-level 2, lexically greater than level 1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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122 * Wiklund_2008 correlation
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123 * Wiklund_2008 covariance
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124 * Galindo_Prieto_2014 VIP for predictive components, VIP[4,p]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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125 * Galindo_Prieto_2014 VIP for orthogonal components, VIP[4,o]
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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126 * (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.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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127 -->
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128 <data name="contrast_corcov" label="${tool.name}_${variableMetadata_in.name}_corcov" format="tabular" />
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129 <!--
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130 tsv2: salience table with columns (experimental feature):
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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131 * feature-ID
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132 * Salient level, i.e., for the feature, the class-level having the greatest median intensity
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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133 * 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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134 * 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.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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135 -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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136 <data name="contrast_salience" label="${tool.name}_${variableMetadata_in.name}_salience" format="tabular" />
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137 </outputs>
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138
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139 <tests>
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140 <test>
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141 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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142 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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143 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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144 <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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145 <param name="facC" value="k10"/>
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146 <param name="pairSigFeatOnly" value="FALSE"/>
2
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147 <param name="labelFeatures" value="3"/>
0
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148 <param name="levCSV" value="k[12],k[3-4]"/>
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149 <param name="matchingC" value="regex"/>
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150 <output name="contrast_corcov">
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151 <assert_contents>
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152 <!-- column-labels line -->
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153 <has_text text="featureID" />
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154 <has_text text="factorLevel1" />
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155 <has_text text="factorLevel2" />
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156 <has_text text="correlation" />
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157 <has_text text="covariance" />
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158 <has_text text="vip4p" />
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159 <has_text text="vip4o" />
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160 <has_text text="level1Level2Sig" />
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161 <!-- first matched line -->
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162 <has_text text="M349.2383T700" />
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163 <has_text text="-0.05007" />
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164 <has_text text="-5.8455" />
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165 <has_text text="0.0961269" />
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diff changeset
166 <has_text text="0.1848301" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
167 <!-- second matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
168 <has_text text="M207.9308T206" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
169 <has_text text="-0.2967565" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
170 <has_text text="-19.56942" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
171 <has_text text="1.6023" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
172 <has_text text="1.35368" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
173 <!-- third matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
174 <has_text text="M211.0607T263" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
175 <has_text text="0.47052" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
176 <has_text text="15.910087" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
177 <has_text text="0.89838" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
178 <has_text text="0.125372" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
179 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
180 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
181 <output name="contrast_salience">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
182 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
183 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
184 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
185 <has_text text="salientLevel" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
186 <has_text text="salientRCV" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
187 <has_text text="salience" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
188 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
189 <has_text text="M349.2383T700" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
190 <has_text text="0.659554" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
191 <has_text text="8.81866595" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
192 <!-- second matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
193 <has_text text="M207.9308T206" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
194 <has_text text="0.0578578" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
195 <has_text text="2.27527985" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
196 <!-- third matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
197 <has_text text="M211.0607T263" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
198 <has_text text="9999" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
199 <has_text text="12.87766096" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
200 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
201 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
202 </test>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
203 <test>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
204 <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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parents:
diff changeset
205 <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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parents:
diff changeset
206 <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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parents:
diff changeset
207 <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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parents:
diff changeset
208 <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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parents:
diff changeset
209 <param name="pairSigFeatOnly" value="TRUE"/>
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
210 <param name="labelFeatures" value="3"/>
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
211 <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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parents:
diff changeset
212 <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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parents:
diff changeset
213 <output name="contrast_corcov">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
214 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
215 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
216 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
217 <has_text text="factorLevel1" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
218 <has_text text="factorLevel2" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
219 <has_text text="correlation" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
220 <has_text text="covariance" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
221 <has_text text="vip4p" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
222 <has_text text="vip4o" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
223 <has_text text="level1Level2Sig" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
224 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
225 <has_text text="M349.2383T700" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
226 <has_text text="-0.99601577" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
227 <has_text text="-947.55795176" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
228 <!-- second matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
229 <has_text text="M207.9308T206" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
230 <has_text text="0.688549" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
231 <has_text text="58.22352" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
232 <has_text text="1.394687" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
233 <has_text text="0.06049885" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
234 <!-- third matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
235 <has_text text="M211.0607T263" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
236 <has_text text="-0.572018" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
237 <has_text text="-14.57769" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
238 <has_text text="0.7780899" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
239 <has_text text="0.3678166776" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
240 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
241 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
242 <output name="contrast_salience">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
243 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
244 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
245 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
246 <has_text text="salientLevel" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
247 <has_text text="salientRCV" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
248 <has_text text="salience" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
249 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
250 <has_text text="M349.2383T700" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
251 <has_text text="0.659554" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
parents:
diff changeset
252 <has_text text="8.81866595" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
253 <!-- 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
254 <has_text text="M207.9308T206" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
255 <has_text text="0.0578578" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
256 <has_text text="2.27527985" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
257 <!-- third matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
258 <has_text text="M211.0607T263" />
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="9999" />
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="12.87766096" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
261 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
262 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
263 </test>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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264 <test>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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265 <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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266 <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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267 <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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268 <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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269 <param name="facC" value="k10"/>
2
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270 <param name="labelFeatures" value="3"/>
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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271 <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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272 <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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273 <output name="contrast_corcov">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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274 <assert_contents>
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275 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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276 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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277 <has_text text="factorLevel1" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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278 <has_text text="factorLevel2" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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279 <has_text text="correlation" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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280 <has_text text="covariance" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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281 <has_text text="vip4p" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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282 <has_text text="vip4o" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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283 <!-- 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
284 <has_text text="M349.2383T700" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
285 <has_text text="-0.64331257" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
286 <has_text text="-161.82220" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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287 <has_text text="1.862455" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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288 <has_text text="0.2105143" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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289 <!-- 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
290 <has_text text="M207.9308T206" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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291 <has_text text="-0.313507" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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292 <has_text text="-20.0476" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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293 <has_text text="1.6956987" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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294 <has_text text="1.19247" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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295 <!-- third matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
296 <has_text text="M211.0607T263" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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297 <has_text text="-0.38986114" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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298 <has_text text="-23.747718" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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299 <has_text text="1.064296856" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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300 <has_text text="1.16507455" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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301 </assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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302 </output>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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303 <output name="contrast_salience">
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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304 <assert_contents>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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305 <!-- column-labels line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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306 <has_text text="featureID" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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307 <has_text text="salientLevel" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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308 <has_text text="salientRCV" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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309 <has_text text="salience" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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310 <!-- first matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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311 <has_text text="M349.2383T700" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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312 <has_text text="0.659554" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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313 <has_text text="8.81866595" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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314 <!-- second matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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315 <has_text text="M207.9308T206" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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316 <has_text text="0.0578578" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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317 <has_text text="2.27527985" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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318 <!-- third matched line -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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319 <has_text text="M211.0607T263" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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320 <has_text text="9999" />
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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321 <has_text text="12.87766096" />
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 </test>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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325 </tests>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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326 <help><![CDATA[
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327
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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328 **Run PLS-DA Contrasts of Univariate Results**
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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329 ----------------------------------------------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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330
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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331 **Author** - Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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332
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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333
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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334 Motivation
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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335 ----------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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336
4
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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diff changeset
337 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 to discriminate to which class a sample should be assigned (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 3.0) include a tool for making the equivalent of an S-PLOT.
0
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338
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339 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).
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340
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341 The primary aims of this tool are:
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342
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343 - To compute and visualize multiple contrasts with OPLS-DA and the covariance vs. correlation plot.
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344 - To write the results to data files for use in further multivariate analysis or visualization.
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345
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346 Note: This tool only supports categorical factors with non-numeric level-names.
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347
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348 Description
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349 -----------
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350
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351 The purpose of the 'PLS-DA Contrasts' tool is to visualize GC-MS or LC-MS features that are possible biomarkers.
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352
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353 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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354 For instance, suppose that you ran Kruskal-Wallis testing for a column named 'cluster' in sampleMetadata that has values 'k1' and 'k2' and at least one other value.
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355
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356 - 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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357 - 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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358
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359 The 'PLS-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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360
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361 **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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362
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363 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, **the preferred workflow is to use univariate testing to exclude features that are not significantly different and 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.
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364
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365 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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366
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367 - picking features with maximum loadings along the projection parallel to the predictor (loadp),
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368 - examining extreme values on S-PLOTs (for which covariance is linearly related to loadp),
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369 - examining "variable importance in projection VIP for OPLS-DA" (Galindo-Prieto *et al.* 2014), and
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370 - examining a feature's "selectivity ratio" (Rajalahti *et al.*, 2009).
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371
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372 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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373
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374 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.
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375
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376 Regardless of how any potential biomarker is identified, further validation analysis (e.g., independent confirmatory experiments) is needed before it is recommended for general application.
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377
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378
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379 W4M Workflow Position
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380 ---------------------
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381
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382 - Upstream tool: **Univariate** (category: Statistical Analysis) or (not generally recommended) any **Preprocessing** tool that produces or updates a 'variableMetadata' file.
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383 - Downstream tool categories: **Statistical Analysis**
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384
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385 Input files
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386 -----------
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387
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388 +----------------------+-----------+
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389 | File | Format |
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390 +======================+===========+
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391 | Data matrix | tabular |
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392 +----------------------+-----------+
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393 | Sample metadata | tabular |
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394 +----------------------+-----------+
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395 | Variable metadata | tabular |
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396 +----------------------+-----------+
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397
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398 Output files
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399 ------------
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400
1
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401 +-------------------------------------------+-----------+
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402 | File | Format |
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403 +===========================================+===========+
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404 | Contrast detail | pdf |
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405 +-------------------------------------------+-----------+
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406 | Contrast "corrlation and covariance" data | tabular |
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407 +-------------------------------------------+-----------+
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408 | Feature "salience" data | tabular |
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409 +-------------------------------------------+-----------+
0
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410
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411 Parameters
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412 ----------
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413
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414 [IN] Data matrix file
1
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415 | 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)
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416 |
0
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417
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418 [IN] Sample metadata file
1
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419 | sample x metadata **sampleMetadata** (tabular separated values) file of the numeric and/or character sample metadata, with '.' as decimal and 'NA' for missing values
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420 |
0
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421
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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422 [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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423 | 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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424 |
0
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425
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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426 [IN] Test
1
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427 | 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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428 | May be one of 'none', 'ttest', 'gwilcoxon', 'anova', 'kruskal', 'pearson', 'spearman'
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429 |
0
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430
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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431 [IN] Factor of interest
1
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432 | 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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433 |
0
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434
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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435 [IN] Retain only pairwise-significant features
5
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436 | *Note that when 'Test' is 'none', all features are included in the analysis and this parameter is not settable.*
1
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437 | 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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438 | 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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439 |
0
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440
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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441 [IN] Levels of interest
1
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442 | 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.
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443 |
0
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444
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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445 [IN] Level-name matching
1
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446 | Indicator of **how levels are to be specified generically** (if at all) - wild cards, regular expressions, or none (no generic matching).
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447 |
0
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448
2
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449 [IN] Label how many extreme features
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450 | 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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451 |
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452
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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453 [OUT] Contrast-detail output PDF
1
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454 | Several plots for each two-projection OPLS-DA analysis:
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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455
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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456 - (top-left) **correlation-versus-covariance plot** of OPLS-DA results (a work-alike for the S-PLOT, computed using formula in Supplement to Wiklund, *op. cit.*); point-color becomes saturated as the "variable importance in projection to the predictive components" (VIP\ :subscript:`4,p` from Galindo-Prieto *et al.* 2014) ranges from 0.83 and 1.21 (Mehmood *et al.* 2012)
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457 - (bottom-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)
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458 - (top-right) OPLS-DA **scores-plot** for the two projections (Th]]>&#233;<![CDATA[venot *et al.*, 2015)
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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459 - (bottom-right) OPLS-DA **loadings-plot** for the two projections (*ibid.*)
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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460
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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461 [OUT] Contrast Correlation-Covarinace data TABULAR
1
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462 | 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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463 | 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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464 | This file has the following columns:
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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465
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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466 - **featureID** - feature-identifier
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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467 - **factorLevel1** - factor-level 1
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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468 - **factorLevel2** - factor-level 2 (or "other" when contrasting factor-level 1 with all other levels)
2
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469 - **correlation** - correlation of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in Supplement to Wiklund, *op. cit.*). Note that, for a given contrast, there is a linear relationship between 'loadp' and 'correlation'.
0
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470 - **covariance** - covariance of the features projection explaining the difference between the features, < 0 when intensity for level 1 is greater (from formula in *ibid.*)
1
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471 - **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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472 - **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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473 - **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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474 - **loado** - variable loading for the orthogonal projection (*ibid.*)
0
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475 - **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
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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476
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477 [OUT] Feature "Salience" data TABULAR
1
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478 | 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 (and unproven) way to identify features that may suggest potential biomarkers without dimensional reduction of 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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479
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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480 - **featureID** - feature identifier
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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481 - **salientLevel** - salient level, i.e., for the feature, the class-level having the greatest median intensity
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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482 - **salientRCV** - 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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483 - **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
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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484
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485 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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486 ---------------------------------------
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487
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488 "wild card" 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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489
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490 - 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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491 - 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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492 - 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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493
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494 For example
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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495
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496 - '``??.le*``' matches '``my.level``' but not '``my.own.level``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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497 - '``*.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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498 - '``*.level``' matches neither '``my.level``' nor '``my.own.level``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
499
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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500 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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501 ------------------------------------------------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
502
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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503 "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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diff changeset
504
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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505 POSIX 1003.2 standard regular expressions allow precise pattern-matching and are exhaustively defined at:
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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506 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
507
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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508 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
509
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
510 - '``^``' 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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diff changeset
511 - '``$``' matches the end of a level-name
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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512 - '``.``' outside of square brackets matches a single character
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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513 - '``*``' matches character specified immediately before zero or more times
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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514 - Square brackets specify a set of characters to be matched. Within square brackets:
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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515
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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516 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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517 - '``-``' is used to specify ranges of characters
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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518
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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519 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
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
520
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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521 First Example: Consider a field of level-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
522
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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523 - 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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diff changeset
524 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-levels as '``front3,marq3``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
525 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-levels as '``front12,marq12``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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526 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-levels as '``front3,front6,front9,marq3,marq6,marq9``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
527
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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528 Second Example: Consider these regular expression patterns as possible matches to a sample-level name '``AB0123``':
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
529
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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530 - '``^[A-Z][A-Z][0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
531 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
532 - '``^[A-Z][0-9]*``' - MATCHES '``**^A** B0123$``' - 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
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diff changeset
533 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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534 - '``^[A-Z][A-Z]*[0-9][0-9]$``' - NO MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
535 - '``^[A-Z][0-9]*$``' - 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
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diff changeset
536
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
537 Working examples
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
538 ----------------
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
539
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
540 **Input files**
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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541
4
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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diff changeset
542 +-------------------------------------------------------------------------------------------------------------------+
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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543 | Download from URL |
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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diff changeset
544 +===================================================================================================================+
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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545 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_dataMatrix.tsv |
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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parents: 3
diff changeset
546 +-------------------------------------------------------------------------------------------------------------------+
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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diff changeset
547 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv |
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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parents: 3
diff changeset
548 +-------------------------------------------------------------------------------------------------------------------+
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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diff changeset
549 | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/input_variableMetadata.tsv |
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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diff changeset
550 +-------------------------------------------------------------------------------------------------------------------+
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
551
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
552 **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
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diff changeset
553
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
554 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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555 | Input Parameter or Result | Value |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
556 +============================================+========================================================================================================================================+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
557 | Factor of interest | k10 |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
558 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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559 | Univariate Significance-Test | kruskal |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
560 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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561 | Retain only pairwise-significant features | Yes |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
562 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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563 | Levels of interest | k[12],k[3-4] |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
564 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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565 | 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
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diff changeset
566 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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567 | Number of features having extreme loadings | ALL |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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568 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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569 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov.tsv |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
570 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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571 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience.tsv |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
572 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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573 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail.pdf |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
574 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
575
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
576 **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
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577
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
578 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
579 | 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
580 +============================================+========================================================================================================================================+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
581 | 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
582 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
583 | 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
584 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
585 | Retain only pairwise-significant features | No |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
586 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
587 | Levels of interest | ``*`` |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
588 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
589 | Level-name matching | use wild cards 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
590 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
591 | Number of features having extreme loadings | 5 |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
592 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
593 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_all.tsv |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
594 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
595 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_all.tsv |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
596 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
597 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_all.pdf |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
598 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
599
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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600 **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
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diff changeset
601
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
602 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
603 | 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
604 +============================================+========================================================================================================================================+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
605 | 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
606 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
607 | Univariate Significance-Test | none |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
608 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
609 | 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
610 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
611 | 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
612 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
613 | Number of features having extreme loadings | 0 |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
614 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
615 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_global.tsv |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
616 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
617 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_global.tsv |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
618 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
619 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_global.pdf |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
620 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
621
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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622 **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
623
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
624 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
625 | 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
626 +============================================+========================================================================================================================================+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
627 | Factor of interest | lohi |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
628 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
629 | Univariate Significance-Test | none |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
630 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
631 | Levels of interest | low,high |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
632 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
633 | 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
634 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
635 | Number of features having extreme loadings | 3 |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
636 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
637 | Output primary table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_corcov_lohi.tsv |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
638 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
639 | Output salience table | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_salience_lohi.tsv |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
640 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
641 | Output figures PDF | https://raw.githubusercontent.com/HegemanLab/w4mcorcov_galaxy_wrapper/master/test-data/expected_contrast_detail_lohi.pdf |
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
eschen42
parents: 0
diff changeset
642 +--------------------------------------------+----------------------------------------------------------------------------------------------------------------------------------------+
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
eschen42
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diff changeset
643
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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parents:
diff changeset
644
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
645 Trademarks
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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646 ----------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
647
4
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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diff changeset
648 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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diff changeset
649
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
650
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
651 Release notes
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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652 -------------
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
653
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
654 0.98.8
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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parents: 4
diff changeset
655
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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diff changeset
656 - new feature: Replace loadings plot with correlation-versus-covariance plot for orthogonal features, i.e., the consistency of features influencing within-treatment variation (which is linearly related to the loading of the orthogonal projection) versus consistency. This eliminates the need for the parameter to suppress labels for features with extreme orthogonal loadings
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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parents: 4
diff changeset
657
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
658 0.98.7
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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parents: 3
diff changeset
659
5
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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diff changeset
660 - bug fix: Handle case of a treatment level with only one sample.
4
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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diff changeset
661
3
5aaab36bc523 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 88004a3cf8868d68da1ec5bd2c1be53746350367
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parents: 2
diff changeset
662 0.98.6
5aaab36bc523 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 88004a3cf8868d68da1ec5bd2c1be53746350367
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parents: 2
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663
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
664 - bug fix: Set 'crossvalI' param (of R function 'ropls::opls') to the number of samples when the there are fewer than seven samples.
3
5aaab36bc523 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 88004a3cf8868d68da1ec5bd2c1be53746350367
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parents: 2
diff changeset
665
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
666 0.98.5
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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parents: 1
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667
5
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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668 - bug fix: Fit feature-labels within clipping region of cor-vs.cov plot
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
669 - new feature: optionally (and by default) suppress labels for features with extreme orthogonal loadings
e03582f26617 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 7682e8e7ae2bfb926d94b414b9a1649389f33582
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670
1
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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671 0.98.3
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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parents: 0
diff changeset
672
5
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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parents: 4
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673 - Add support for two-level factors
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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674 - Add adjusted mz and rt to output tables
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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diff changeset
675 - Allow explicitly setting the number of features with extreme loadings to be labelled on the correlation vs. covariance plot
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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parents: 4
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676 - Add loadings to corcov table
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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677
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
678 0.98.2
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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679
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
680 - first release
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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681
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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682
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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683 ]]></help>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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684 <citations>
5
50f60f94c034 planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit aff1790e25523d038a1e9528de748191c096132f
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685 <!-- 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
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686 <citation type="doi">10.5281/zenodo.1034784</citation>
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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687 <!-- 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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688 <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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689 <!-- 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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690 <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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691 <!-- 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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692 <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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693 <!-- 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
694 <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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695 <!-- Rajalahti_2009 Biomarker discovery using selectivity ratio -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
696 <citation type="doi">10.1016/j.chemolab.2008.08.004</citation>
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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697 <!-- Rinuardo 2016 -->
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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698 <citation type="doi">10.3389/fmolb.2016.00026</citation>
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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699 <!-- Sun_2016 Urinary Biomarkers for adolescent idiopathic scoliosis -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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700 <citation type="doi">10.1038/srep22274</citation>
4
8bba31f628da planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 8f2dc8b66666340275cd8967e09c504720528462
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701 <!-- Thevenot_2015 Urinary metabolome statistics -->
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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702 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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703 <!-- ropls package -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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704 <citation type="bibtex"><![CDATA[
1
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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705 @incollection{Thevenot_ropls_2017,
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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706 author = {Th{\'{e}}venot, Etienne A.},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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707 title = {ropls: PCA, PLS(-DA) and OPLS(-DA) for multivariate analysis and feature selection of omics data},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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708 publisher = {bioconductor.org},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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709 year = {2017},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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710 doi = {10.18129/B9.bioc.ropls},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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711 booktitle = {Bioconductor: Open source software for bioinformatics},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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diff changeset
712 address = {Roswell Park Cancer Institute},
0c2ad44b6c9c planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit 01d4a951cf09e7b88fcec96b8043bc7568cc5c92
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713 }
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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714 ]]></citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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715 <!-- Wiklund_2008 OPLS PLS-DA and S-PLOT -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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diff changeset
716 <citation type="doi">10.1021/ac0713510</citation>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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717 </citations>
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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718 <!--
5
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diff changeset
719 vim:noet:sw=2:ts=2
0
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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720 -->
23f9fad4edfc planemo upload for repository https://github.com/HegemanLab/w4mcorcov_galaxy_wrapper/tree/master commit bd26542b811de06c1a877337a2840a9f899c2b94
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721 </tool>