Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 13:c18040b6e8b9 draft

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"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
author eschen42
date Thu, 24 Oct 2019 10:21:23 -0400
parents 38f509903a0b
children 87ec0d3c2266
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13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.14">
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2 <description>Filter W4m data by values or metadata</description>
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3 <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ -->
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4 <requirements>
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5 <requirement type="package" version="3.6.1">r-base</requirement>
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6 <requirement type="package" version="1.1_5">r-batch</requirement>
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7 <requirement type="package" version="0.98.14">w4mclassfilter</requirement>
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8 </requirements>
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9 <command detect_errors="aggressive"><![CDATA[
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10 unset R_HOME;
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11 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
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12 dataMatrix_in '$dataMatrix_in'
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13 sampleMetadata_in '$sampleMetadata_in'
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14 variableMetadata_in '$variableMetadata_in'
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15 sampleclassNames '$sampleclassNames'
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16 inclusive '$inclusive'
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17 wildcards '$wildcards'
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18 classnameColumn '$classnameColumn'
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19 samplenameColumn 'sampleMetadata'
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20 variable_range_filter '$variableRangeFilter'
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21 transformation '$transformation'
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22 imputation '$imputation'
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23 dataMatrix_out '$dataMatrix_out'
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24 sampleMetadata_out '$sampleMetadata_out'
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25 variableMetadata_out '$variableMetadata_out'
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26 order_vrbl '$order_vrbl'
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27 order_smpl '$order_smpl'
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28 ]]></command>
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29 <inputs>
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30 <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"
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31 help="data matrix, with sample names in first row and feature names in first column" />
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32 <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data"
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33 help="sample metadata, with one row per sample" />
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34 <param name="variableMetadata_in" format="tabular" label="Variable metadata file" type="data"
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35 help="variable metadata, with one row per feature" />
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36 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class"
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37 help="name of the column in sample metadata that has the values to be tested against the 'Names of sample-classes' input parameter">
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38 <sanitizer>
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39 <valid initial="string.letters">
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40 <add preset="string.digits"/>
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41 <add value="&#46;" /> <!-- dot, period -->
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42 <add value="&#95;" /> <!-- underscore -->
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43 </valid>
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44 </sanitizer>
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45 </param>
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46 <param name="sampleclassNames" label="Names of sample-classes" type="text" value = ""
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47 help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out (Leave empty to match no names.)">
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48 <sanitizer>
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49 <valid initial="string.letters">
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50 <add preset="string.digits"/>
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51 <add value="&#123;" /> <!-- l-cube, left-curly-bracket -->
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52 <add value="&#124;" /> <!-- pipe -->
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53 <add value="&#125;" /> <!-- r-cube, right-curly-bracket -->
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54 <add value="&#36;" /> <!-- dollar, dollar-sign -->
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55 <add value="&#40;" /> <!-- left-paren -->
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56 <add value="&#41;" /> <!-- right-paren -->
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57 <add value="&#42;" /> <!-- splat, asterisk -->
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58 <add value="&#43;" /> <!-- plus -->
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59 <add value="&#45;" /> <!-- dash, hyphen -->
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60 <add value="&#44;" /> <!-- comma -->
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61 <add value="&#46;" /> <!-- dot, period -->
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62 <add value="&#58;" /> <!-- colon -->
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63 <add value="&#59;" /> <!-- semi, semicolon -->
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64 <add value="&#63;" /> <!-- what, question mark -->
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65 <add value="&#91;" /> <!-- l-squib, left-squre-bracket -->
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66 <add value="&#92;" /> <!-- whack, backslash -->
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67 <add value="&#93;" /> <!-- r-squib, right-squre-bracket -->
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68 <add value="&#94;" /> <!-- hat, caret -->
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69 <add value="&#95;" /> <!-- underscore -->
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70 </valid>
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71 </sanitizer>
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72 </param>
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73 <param name="wildcards" label="Use 'wild cards' or 'regular expressions'" type="select"
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74 help="'wild-cards' - use '*' and '?' to match class names; &#160;&#160; 'regular-expressions' - use regular expressions to match class names">
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75 <option value="TRUE" selected="true">wild-cards</option>
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76 <option value="FALSE">regular-expressions</option>
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77 </param>
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78 <param name="inclusive" label="Exclude/include named classes" type="select"
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79 help="'filter-out' - exclude only the named sample-classes; &#160;&#160; 'filter-in' - include only the named sample-classes">
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80 <option value="TRUE">filter-in</option>
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81 <option value="FALSE" selected="true">filter-out</option>
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82 </param>
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83 <param name="variableRangeFilter" label="Variable-range filters" type="text" value = ""
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84 help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max' (leave empty for no filtering, as described in help below.)">
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85 <sanitizer>
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86 <valid initial="string.letters">
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87 <add preset="string.digits"/>
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88 <add value="&#44;" /> <!-- comma -->
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89 <add value="&#46;" /> <!-- dot, period -->
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90 <add value="&#58;" /> <!-- colon -->
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91 <add value="&#95;" /> <!-- underscore -->
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92 </valid>
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93 </sanitizer>
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94 </param>
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95 <param name="transformation" label="Data-transformation" type="select"
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96 help="'none' - do not transform data; &#160;&#160; 'log2' - log base 2 of data; &#160;&#160; 'log10' - log base 10 of data; &#160;&#160; in all cases, negative and missing values are imputed to zero">
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97 <option value="none" selected="true">none</option>
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98 <option value="log2">log2</option>
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99 <option value="log10">log10</option>
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100 </param>
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101 <param name="imputation" label="Imputation of missing values" type="select"
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102 help="'zero' - replace missing values with zero; &#160;&#160; 'center' - replace missing values with feature-median; &#160;&#160; 'none' - perform no imputation">
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103 <option value="zero" selected="true">zero</option>
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104 <option value="center">center</option>
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105 <option value="none">none</option>
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106 </param>
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107 <param name="order_smpl" label="Column that specifies order for samples" type="text" value = "sampleMetadata"
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108 help="name of the column in sample metadata that is used to sort samples">
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109 <sanitizer>
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110 <valid initial="string.letters">
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111 <add preset="string.digits"/>
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112 <add value="&#46;" /> <!-- dot, period -->
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113 <add value="&#95;" /> <!-- underscore -->
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114 </valid>
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115 </sanitizer>
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116 </param>
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117 <param name="order_vrbl" label="Column that specifies order for features" type="text" value = "variableMetadata"
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118 help="name of the column in variable metadata that is used to sort features">
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119 <sanitizer>
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120 <valid initial="string.letters">
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121 <add preset="string.digits"/>
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122 <add value="&#46;" /> <!-- dot, period -->
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123 <add value="&#95;" /> <!-- underscore -->
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124 </valid>
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125 </sanitizer>
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126 </param>
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127 </inputs>
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128 <outputs>
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129 <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>
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130 <data name="sampleMetadata_out" format="tabular" label="${sampleMetadata_in.name}.subset" ></data>
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131 <data name="variableMetadata_out" format="tabular" label="${variableMetadata_in.name}.subset" ></data>
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132 </outputs>
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133 <tests>
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134 <!-- test 1 -->
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135 <test>
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136 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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137 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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138 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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139 <param name="classnameColumn" value="gender"/>
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140 <param name="sampleclassNames" value="M"/>
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141 <param name="wildcards" value="FALSE"/>
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142 <param name="inclusive" value="TRUE"/>
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143 <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/>
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144 <param name="transformation" value="none"/>
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145 <output name="dataMatrix_out">
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146 <assert_contents>
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147 <has_text text="747080" />
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148 <not_has_text text="13420742" />
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149 <not_has_text text="47259" />
10
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150 </assert_contents>
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151 </output>
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152 <output name="sampleMetadata_out">
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153 <assert_contents>
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154 <has_text text="HU_017" />
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155 <has_text text="HU_034" />
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156 <has_text text="HU_078" />
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157 <has_text text="HU_091" />
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158 <has_text text="HU_093" />
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159 <has_text text="HU_099" />
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160 <has_text text="HU_130" />
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161 <has_text text="HU_134" />
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162 <has_text text="HU_138" />
10
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163 <not_has_text text="HU_028" />
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164 <not_has_text text="HU_051" />
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165 <not_has_text text="HU_060" />
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166 <not_has_text text="HU_110" />
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167 <not_has_text text="HU_149" />
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168 <not_has_text text="HU_152" />
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169 <not_has_text text="HU_175" />
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170 <not_has_text text="HU_178" />
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171 <not_has_text text="HU_185" />
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172 <not_has_text text="HU_204" />
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173 <not_has_text text="HU_208" />
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174 </assert_contents>
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175 </output>
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176 <output name="variableMetadata_out">
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177 <assert_contents>
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178 <has_text text="HMDB00208" />
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179 <has_text text="HMDB01032" />
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180 <has_text text="HMDB01101.1" />
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181 <has_text text="HMDB13189" />
10
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182 <not_has_text text="HMDB00191" />
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183 <not_has_text text="HMDB00251" />
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184 <not_has_text text="HMDB00299" />
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185 <not_has_text text="HMDB00512" />
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186 <not_has_text text="HMDB00518" />
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187 <not_has_text text="HMDB00715" />
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188 <not_has_text text="HMDB00822" />
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189 <not_has_text text="HMDB03193" />
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190 <not_has_text text="HMDB04824" />
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191 <not_has_text text="HMDB10348" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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192 <not_has_text text="HMDB59717" />
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193 </assert_contents>
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194 </output>
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195 </test>
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196 <!-- test 2 -->
12
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197 <test>
10
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198 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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199 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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200 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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201 <!-- test that hyphens in regular expressions work -->
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202 <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/>
12
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203 <param name="inclusive" value="TRUE"/>
10
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204 <param name="wildcards" value="FALSE"/>
12
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205 <param name="classnameColumn" value="sampleMetadata"/>
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206 <!-- test that variableRangeFilter works with tranformation -->
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207 <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
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208 <param name="transformation" value="log10"/>
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209 <param name="imputation" value="zero"/>
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210 <output name="dataMatrix_out" md5="5644d2ea01d072ee1d0c40e29e9d0089">
10
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211 <assert_contents>
12
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212 <has_text text="5.8733671" />
10
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213 </assert_contents>
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214 </output>
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215 <output name="sampleMetadata_out">
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216 <assert_contents>
12
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217 <has_text text="HU_017" />
10
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218 <has_text text="HU_028" />
12
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219 <has_text text="HU_034" />
10
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220 <has_text text="HU_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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221 <has_text text="HU_060" />
12
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222 <has_text text="HU_078" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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223 <has_text text="HU_091" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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224 <has_text text="HU_093" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
225 <has_text text="HU_099" />
10
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226 <has_text text="HU_110" />
12
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227 <has_text text="HU_130" />
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228 <has_text text="HU_134" />
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229 <has_text text="HU_138" />
10
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230 <has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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231 <has_text text="HU_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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232 <has_text text="HU_175" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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233 <has_text text="HU_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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234 <has_text text="HU_185" />
12
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235 <has_text text="HU_208" />
10
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236 <not_has_text text="HU_204" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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237 </assert_contents>
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238 </output>
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239 <output name="variableMetadata_out">
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240 <assert_contents>
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diff changeset
241 <has_text text="HMDB00191" />
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242 <has_text text="HMDB00208" />
12
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diff changeset
243 <has_text text="HMDB01032" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
244 <has_text text="HMDB01101.1" />
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diff changeset
245 <has_text text="HMDB13189" />
10
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diff changeset
246 <not_has_text text="HMDB00251" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
247 <not_has_text text="HMDB00299" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
248 <not_has_text text="HMDB00512" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
249 <not_has_text text="HMDB00518" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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250 <not_has_text text="HMDB00715" />
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251 <not_has_text text="HMDB00822" />
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252 <not_has_text text="HMDB03193" />
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253 <not_has_text text="HMDB04824" />
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254 <not_has_text text="HMDB10348" />
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255 <not_has_text text="HMDB59717" />
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256 </assert_contents>
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257 </output>
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258 </test>
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259 <!-- test 3 -->
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260 <test>
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261 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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262 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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263 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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264 <param name="classnameColumn" value="gender"/>
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265 <param name="sampleclassNames" value="M"/>
12
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266 <param name="inclusive" value="TRUE"/>
10
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267 <param name="transformation" value="none"/>
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268 <output name="dataMatrix_out">
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269 <assert_contents>
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270 <not_has_text text="HU_028" />
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271 <not_has_text text="HU_051" />
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272 <not_has_text text="HU_060" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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273 <not_has_text text="HU_110" />
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274 <not_has_text text="HU_149" />
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275 <not_has_text text="HU_152" />
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276 <not_has_text text="HU_175" />
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277 <not_has_text text="HU_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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278 <not_has_text text="HU_185" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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279 <not_has_text text="HU_204" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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280 <not_has_text text="HU_208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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281 <has_text text="HU_017" />
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282 <has_text text="HU_034" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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283 <has_text text="HU_078" />
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284 <has_text text="HU_091" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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285 <has_text text="HU_093" />
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286 <has_text text="HU_099" />
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287 <has_text text="HU_130" />
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288 <has_text text="HU_134" />
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289 <has_text text="HU_138" />
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290 <has_text text="HMDB03193" />
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291 <not_has_text text="HMDB00822" />
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292 <has_text text="HMDB01101" />
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293 <has_text text="HMDB01101.1" />
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294 <has_text text="HMDB10348" />
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295 <has_text text="HMDB59717" />
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296 <has_text text="HMDB13189" />
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297 <has_text text="HMDB00299" />
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298 <has_text text="HMDB00191" />
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299 <has_text text="HMDB00518" />
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300 <has_text text="HMDB00715" />
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301 <has_text text="HMDB01032" />
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302 <has_text text="HMDB00208" />
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303 <has_text text="HMDB04824" />
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304 <has_text text="HMDB00512" />
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305 <has_text text="HMDB00251" />
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306 </assert_contents>
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307 </output>
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308 </test>
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309 <!-- test 4 -->
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310 <test>
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311 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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312 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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313 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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314 <param name="classnameColumn" value="gender"/>
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315 <param name="sampleclassNames" value="*"/>
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316 <param name="wildcards" value="TRUE"/>
12
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317 <param name="inclusive" value="TRUE"/>
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318 <param name="imputation" value="zero"/>
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319 <output name="dataMatrix_out" md5="b2eac4946d3803a07606286b50451af4">
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320 <assert_contents>
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321 <not_has_text text="NA" />
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322 </assert_contents>
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323 </output>
10
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324 <output name="sampleMetadata_out">
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325 <assert_contents>
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326 <not_has_text text="HU_204" />
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327 <has_text text="HU_028" />
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328 <has_text text="HU_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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329 <has_text text="HU_060" />
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330 <has_text text="HU_110" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
331 <has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
332 <has_text text="HU_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
333 <has_text text="HU_175" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
334 <has_text text="HU_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
335 <has_text text="HU_185" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
336 <has_text text="HU_208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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337 <has_text text="HU_017" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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338 <has_text text="HU_034" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
339 <has_text text="HU_078" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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340 <has_text text="HU_091" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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341 <has_text text="HU_093" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
342 <has_text text="HU_099" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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343 <has_text text="HU_130" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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344 <has_text text="HU_134" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
345 <has_text text="HU_138" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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346 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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347 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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348 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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349 <!-- test 5 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
350 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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351 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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352 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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353 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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354 <param name="classnameColumn" value="gender"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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355 <param name="sampleclassNames" value="M"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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356 <param name="wildcards" value="FALSE"/>
12
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357 <param name="inclusive" value="TRUE"/>
10
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358 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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359 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
360 <not_has_text text="HU_028" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
361 <not_has_text text="HU_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
362 <not_has_text text="HU_060" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
363 <not_has_text text="HU_110" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
364 <not_has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
365 <not_has_text text="HU_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
366 <not_has_text text="HU_175" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
367 <not_has_text text="HU_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
368 <not_has_text text="HU_185" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
369 <not_has_text text="HU_204" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
370 <not_has_text text="HU_208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
371 <has_text text="HU_017" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
372 <has_text text="HU_034" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
373 <has_text text="HU_078" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
374 <has_text text="HU_091" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
375 <has_text text="HU_093" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
376 <has_text text="HU_099" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
377 <has_text text="HU_130" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
378 <has_text text="HU_134" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
379 <has_text text="HU_138" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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380 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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381 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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382 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
383 <!-- test 6 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
384 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
385 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
386 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
387 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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388 <param name="classnameColumn" value="gender"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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389 <param name="sampleclassNames" value="M"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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390 <param name="wildcards" value="FALSE"/>
12
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diff changeset
391 <param name="inclusive" value="TRUE"/>
10
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diff changeset
392 <output name="variableMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
393 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
394 <has_text text="HMDB03193" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
395 <not_has_text text="HMDB00822" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
396 <has_text text="HMDB01101" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
397 <has_text text="HMDB01101.1" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
398 <has_text text="HMDB10348" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
399 <has_text text="HMDB59717" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
400 <has_text text="HMDB13189" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
401 <has_text text="HMDB00299" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
402 <has_text text="HMDB00191" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
403 <has_text text="HMDB00518" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
404 <has_text text="HMDB00715" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
405 <has_text text="HMDB01032" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
406 <has_text text="HMDB00208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
407 <has_text text="HMDB04824" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
408 <has_text text="HMDB00512" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
409 <has_text text="HMDB00251" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
410 </assert_contents>
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diff changeset
411 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
412 </test>
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diff changeset
413 <!-- test 7 -->
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diff changeset
414 <test>
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diff changeset
415 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
416 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
417 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
418 <param name="classnameColumn" value="gender"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
419 <param name="sampleclassNames" value="M"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
420 <param name="wildcards" value="FALSE"/>
12
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diff changeset
421 <param name="inclusive" value="TRUE"/>
10
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diff changeset
422 <output name="variableMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
423 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
424 <has_text text="HMDB03193" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
425 <not_has_text text="HMDB00822" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
426 <has_text text="HMDB01101" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
427 <has_text text="HMDB01101.1" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
428 <has_text text="HMDB10348" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
429 <has_text text="HMDB59717" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
430 <not_has_text text="HMDB13189" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
431 <has_text text="HMDB00299" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
432 <has_text text="HMDB00191" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
433 <has_text text="HMDB00518" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
434 <has_text text="HMDB00715" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
435 <has_text text="HMDB01032" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
436 <has_text text="HMDB00208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
437 <has_text text="HMDB04824" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
438 <has_text text="HMDB00512" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
439 <has_text text="HMDB00251" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
440 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
441 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
442 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
443 <!-- test 8 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
444 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
445 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
446 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
447 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
448 <param name="classnameColumn" value="gender"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
449 <param name="sampleclassNames" value="[Mm],[fF]"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
450 <param name="wildcards" value="FALSE"/>
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
451 <param name="inclusive" value="TRUE"/>
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
452 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
453 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
454 <has_text text="HU_028" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
455 <has_text text="HU_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
456 <has_text text="HU_060" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
457 <has_text text="HU_110" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
458 <has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
459 <has_text text="HU_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
460 <has_text text="HU_175" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
461 <has_text text="HU_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
462 <has_text text="HU_185" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
463 <not_has_text text="HU_204" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
464 <has_text text="HU_208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
465 <has_text text="HU_017" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
466 <has_text text="HU_034" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
467 <has_text text="HU_078" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
468 <has_text text="HU_091" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
469 <has_text text="HU_093" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
470 <has_text text="HU_099" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
471 <has_text text="HU_130" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
472 <has_text text="HU_134" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
473 <has_text text="HU_138" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
474 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
475 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
476 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
477 <!-- test 9 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
478 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
479 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
480 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
481 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
482 <param name="classnameColumn" value=""/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
483 <param name="sampleclassNames" value="M"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
484 <param name="wildcards" value="FALSE"/>
12
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parents: 11
diff changeset
485 <param name="inclusive" value="TRUE"/>
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
486 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
487 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
488 <has_text text="HU_028" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
489 <has_text text="HU_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
490 <has_text text="HU_060" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
491 <has_text text="HU_110" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
492 <has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
493 <has_text text="HU_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
494 <has_text text="HU_175" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
495 <has_text text="HU_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
496 <has_text text="HU_185" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
497 <not_has_text text="HU_204" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
498 <has_text text="HU_208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
499 <has_text text="HU_017" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
500 <has_text text="HU_034" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
501 <has_text text="HU_078" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
502 <has_text text="HU_091" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
503 <has_text text="HU_093" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
504 <has_text text="HU_099" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
505 <has_text text="HU_130" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
506 <has_text text="HU_134" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
507 <has_text text="HU_138" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
508 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
509 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
510 </test>
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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511 <!-- test 10 - extends test4 with no imputation rather than zero imputation -->
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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512 <test>
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513 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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514 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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515 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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516 <param name="classnameColumn" value="gender"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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517 <param name="sampleclassNames" value="*"/>
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518 <param name="wildcards" value="TRUE"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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519 <param name="inclusive" value="TRUE"/>
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520 <param name="imputation" value="none"/>
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521 <output name="dataMatrix_out" md5="cc9ab8bdb70b68b43b19b7327d285166">
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522 <assert_contents>
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523 <not_has_text text="HU_204" />
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diff changeset
524 <has_text text="NA" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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525 <has_text text="HU_028" />
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526 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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527 </output>
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528 <output name="sampleMetadata_out">
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529 <assert_contents>
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530 <not_has_text text="HU_204" />
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531 <has_text text="HU_028" />
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532 </assert_contents>
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533 </output>
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534 </test>
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535 <!-- test 11 - extends test4 with center imputation rather than zero imputation -->
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536 <test>
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537 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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538 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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539 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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540 <param name="classnameColumn" value="gender"/>
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541 <param name="sampleclassNames" value="*"/>
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542 <param name="wildcards" value="TRUE"/>
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543 <param name="inclusive" value="TRUE"/>
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544 <param name="imputation" value="center"/>
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545 <output name="dataMatrix_out" md5="75a4802bb8887709e4d4dec8c2c3d3cf">
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546 <assert_contents>
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547 <not_has_text text="HU_204" />
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548 <not_has_text text="NA" />
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549 <has_text text="HU_028" />
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550 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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551 </output>
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552 <output name="sampleMetadata_out">
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553 <assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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554 <not_has_text text="HU_204" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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555 <has_text text="HU_028" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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556 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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557 </output>
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558 </test>
10
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559 </tests>
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560 <help><![CDATA[
0
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561
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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562
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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563 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
0
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564
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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565 --------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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566
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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567
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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568 **R package**
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569
8
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570 The *w4mclassfilter* package (which is used by the W4m Data Subset tool) is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
0
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571
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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572 -----------------------------------------------------------------------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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573
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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574
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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575 **Tool updates**
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576
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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577 See https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper#news
0
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578
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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579 ---------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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580
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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581 ===========================================================
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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582 "W4m Data Subset" - Filter Workflow4Metabolomics data files
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583 ===========================================================
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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584
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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585 ----------
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diff changeset
586 Motivation
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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587 ----------
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588
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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589 GC-MS and LC-MS experiments seek to resolve as features chemicals that have distinct chromatographic retention-time ("rt") and (after ionization) mass-to-charge ratio ("m/z" or "mz").
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590 (If the MS protocol includes fragmentation, several features may result for each chemical.)
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591 Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of rt and m/z.
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592 Ideally, features would be sufficiently reproducible among sample-runs to distinguish features that are commmon among samples from those that differ.
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593
10
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diff changeset
594 The chromatographic retention-time for a chemical can vary from one chromatography run to the next.
8
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595 Workflow4Metabolomics (W4m, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017]) is a "flavor" of Galaxy that uses the XCMS preprocessing tools for "retention-time correction" to align features among samples.
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
596 Features may be better aligned if pooled samples and blanks are included.
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597
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diff changeset
598 Multivariate statistical techniques may be used to discover clusters of similar samples (Th]]>&#233;<![CDATA[venot *et al.*, 2015).
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diff changeset
599 However, once retention-time alignment of features has been achieved among samples in GC-MS and LC-MS datasets:
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600
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601 - The presence of pools and blanks may confound identification and separation of clusters.
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602 - Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance.
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603
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604 -----------
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605 Description
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606 -----------
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607
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608 The **W4m Data Subset** tool **selects subsets of samples, features, or data values** for further analysis.
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609
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610 - The tool takes as input the data matrix, sample metadata, and variable metadata datasets produced by W4m's XCMS [Smith *et al.*, 2006] and CAMERA [Kuhl *et al.*, 2012] tools.
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611 - The tool produces the same trio of output datasets, modified as follows.
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612
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613 This tool can perform several operations to reduce the number samples or features to be analyzed (although **this should be done only in a statistically sound manner** consistent with the nature of the experiment):
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614
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615 - Samples may be eliminated by filtering on a designated “sample class” column in sampleMetadata.
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616 - Features may be eliminated by specifying minimum or maximum value (or both) allowable in columns of variableMetadata.
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617 - Features may be eliminated by “range of row-maximum for each feature”, i.e., by specifying minimum or maximum intensity (or both) allowable in each row of the dataMatrix (i.e., for the feature across all samples).
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618
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619 This tool also performs several operations to address several data issues that may impede downstream statistical analysis:
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620
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621 - Samples that are missing from either sampleMetadata or dataMatrix are eliminated.
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622 - Features that are missing from either variableMetadata or dataMatrix are eliminated.
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623 - Features and samples that have zero variance are eliminated.
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624 - Samples and features have consistent order in `variableMetadata`, `sampleMetadata`, and `dataMatrix`.
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625 (The column for sorting `variableMetadata` or `sampleMetadata` may be specified.)
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626 - The names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata".
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627 - If desired, the values in the dataMatrix may be log-transformed.
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628 - If desired, each missing value in dataMatrix is replaced with zero or the median value observed for the corresponding feature.
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629
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630 This tool may be applied several times sequentially, which may be useful for:
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631
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632 - analyzing subsets of samples for progressively smaller sets of treatment-levels, or
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633 - choosing subsets of samples based on criteria in several columns of the sampleMetadata table.
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634
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635 -----------------
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636 Workflow Position
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637 -----------------
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638
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639 This tool can be used at any point downstream of Preprocessing.
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640
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641 - Possible upstream tool categories: Preprocessing, Quality Control, Statistical Analysis, Filter and Sort
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642 - Possible downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
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643
0
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644 -----------
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645 Input files
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646 -----------
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647
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648 +---------------------------+------------+
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649 | File | Format |
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650 +===========================+============+
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651 | Data matrix | tabular |
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652 +---------------------------+------------+
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653 | Sample metadata | tabular |
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654 +---------------------------+------------+
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655 | Variable metadata | tabular |
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656 +---------------------------+------------+
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657
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658
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659 ----------
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660 Parameters
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661 ----------
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662
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663 Data matrix file
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664 | feature x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with period-character ('.') as decimal, and 'NA' for missing values; the table must not contain metadata apart from the required row and column names; the row and column names must be identical (with regard to both content or order) to the respective rownames of the sample metadata file and variable metadata file
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665 |
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666
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667 Sample metadata file
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668 | 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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669 |
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670
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671 Variable metadata file
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672 | variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
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673 |
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674
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675 Column that names the sample-class (default = '``class``')
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676 | name of the column in **sampleMetadata** that has the values to be tested against the '``Names of sample-classes``' input parameter; only letters, digits, periods, and underscores are permitted.
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677 |
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678
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679 Names of sample-classes (default = no names)
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680 | comma-separated names (or regular expressions to match names) of sample-classes to include or exclude
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681 |
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682
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683 'Wild cards' or 'regular expressions' (default = '``wild-cards``')
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684 | '``wild-cards``' - use wild cards to match names of sample-classes (see the 'Wild card patterns to match class-names' section below)
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685 | '``regular-expressions``' - use regular expressions to match the named sample-classes (see the 'Regular expression patterns to match class-names' section below)
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686 |
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687
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688 Exclude/include named classes (default = '``filter-out``')
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689 | '``filter-in``' - include only the named sample-classes
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690 | '``filter-out``' - exclude only the named sample-classes
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691 |
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692
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693 Variable-range filters (default = no filters)
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694 | comma-separated names of variable-range filters (see the 'Variable-range filters' section below)
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695 |
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696
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697 Data-transformation (default = '``none``')
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698 | '``none``' - Do not transform data matrix values.
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699 | '``log2``' - Take the log base 2 of the values in the data matrix.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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700 | '``log10``' - Take the log base 10 of the values in the data matrix.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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701 |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
702
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
703 Data-imputation (default = '``zero``')
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
704 | '``none``' - Do not impute data matrix values.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
705 | '``zero``' - Negative and missing values are imputed to zero.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
706 | '``center``' - For each feature, negative and missing values are imputed to the median of other values.
8
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diff changeset
707 |
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
708
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
709 Column that specifies order for samples (default = 'sampleMetadata')
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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parents: 12
diff changeset
710 | name of the column in **sampleMetadata** that is used to sort samples; only letters, digits, periods, and underscores are permitted.
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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parents: 12
diff changeset
711 |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
712
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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parents: 12
diff changeset
713 Column that specifies order for features (default = 'variableMetadata')
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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parents: 12
diff changeset
714 | name of the column in **variableMetadata** that is used to sort features; only letters, digits, periods, and underscores are permitted.
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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parents: 12
diff changeset
715 |
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
716
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
717 ------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
718 Output files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
719 ------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
720
2
23c6d271def9 planemo upload
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parents: 0
diff changeset
721 sampleMetadata
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
722 | (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples that have been filtered out (by the sample-class filter, or because of zero variance, or because they were missing in the input data matrix)
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
723 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
724
2
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diff changeset
725 variableMetadata
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
726 | (tabular separated values) file identical to the **variableMetadata** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (by the variable-range filter, or because of zero variance, or because they were missing in the input data matrix)
2
23c6d271def9 planemo upload
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diff changeset
727 |
23c6d271def9 planemo upload
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diff changeset
728
23c6d271def9 planemo upload
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diff changeset
729 dataMatrix
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
730 | (tabular separated values) file identical to the **dataMatrix** file given as an input argument, excepting lacking rows and columns for variables and samples that have been filtered out, respectively
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
731 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
732
2
23c6d271def9 planemo upload
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diff changeset
733
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
734 -----------------------------------------
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
735 'Wild card' patterns to match class-names
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
736 -----------------------------------------
4
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diff changeset
737
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
738 W4m Data Subset supports use of R "wild card" patterns to select class-names.
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
739
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
740 - use '``?``' to match a single character
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
741 - use '``*``' to match zero or more characters
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
742 - the entire pattern must match the sample name
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
743
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
744 For example
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
745
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
746 - '``??.samp*``' matches '``my.sample``' but not '``my.own.sample``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
747 - '``*.sample``' matches '``my.sample``' and '``my.own.sample``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
748 - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
749
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
750 --------------------------------------------------
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
751 'Regular expression' patterns to match class-names
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
752 --------------------------------------------------
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
753
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
754 W4m Data Subset supports use of R "regular expression" patterns to select class-names.
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
755
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
756 R uses POSIX 1003.2 standard regular expressions, which allow precise pattern-matching and are exhaustively defined at:
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
757 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
758
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
759 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
760
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
761 - '``^``' matches the beginning of a class-name
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
762 - '``$``' matches the end of a class-name
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
763 - '``.``' outside of square brackets matches a single character
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
764 - '``*``' matches character specified immediately before zero or more times
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
765 - square brackets specify a set of characters to be matched.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
766
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
767 Within square brackets
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
768
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
769 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
770 - '``-``' is used to specify ranges of characters
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
771
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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772 Caveat: The tool wrapper uses the comma ('``,``') to split a list of sample-class names, so **commas may not be used within regular expressions for this tool**
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
773
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
774 First Example: Consider a field of class-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
775
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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776 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
777 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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778 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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779 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-classes as '``front3,front6,front9,marq3,marq6,marq9``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
780
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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781 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
782
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
783 - '``^[A-Z][A-Z][0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
784 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
785 - '``^[A-Z][0-9]*``' - MATCHES '``**^A** B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
786 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
787 - '``^[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.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
788 - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
789
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
790 ----------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
791 Variable-range filters
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
792 ----------------------
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
793
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
794 An array of range-specification strings may be supplied in the `variableRangeFilter`
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
795 argument. If supplied, only features having numerical values in the specified column
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
796 of `variableMetadata` that fall within the specified ranges will be retained
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
797 in the output. Each range is a string of three colon-separated values (e.g., "mz:200:800") in the
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
798 following order:
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
799
11
9f5c0e23c205 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 32cf96ed6c39a93eb9c6cf00494b128bd3c3febe
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diff changeset
800 - the **name of a column of `variableMetadata`** which must have numerical data (only letters, digits, periods, and underscores are permitted in the name itself), e.g., 'mz';
9f5c0e23c205 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 32cf96ed6c39a93eb9c6cf00494b128bd3c3febe
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diff changeset
801 - the **minimum allowed value** in that column for the feature to be retained, e.g., '200';
9f5c0e23c205 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 32cf96ed6c39a93eb9c6cf00494b128bd3c3febe
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diff changeset
802 - the **maximum allowed value**, e.g., '800'.
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
803
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
804 Note for the range specification strings:
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
805
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
806 - **If the "maximum" is less than the "minimum", then the range is exclusive** (e.g., "mz:800:200" means retain only features whose mz is NOT in the range 200-800)
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
807 - **If the name supplied in the first field is 'FEATMAX',** then the string is defining the minimum (and possibly, though less useful, maximum) intensity for each feature in the dataMatrix. For example, "FEATMAX:1e6:" would specify that any feature would be excluded if no sample had an intensity for that feature greater than 1000000.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
808
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
809 - Note, however, that when the "maximum" is greater than the "minimum" for the FEATMAX range specification, then the specification is ignored.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
810
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
811 ----------------------------------
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
812 Data transformation and imputation
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
813 ----------------------------------
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
814
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
815 Data may optionally be log2- or log10-transformed.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
816
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
817 Negative intensity values are always substituted with zeros.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
818
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
819 Missing intensity data values may optionally be imputed. Missing values may be substituted with zeros (as may be appropriate for univariate analysis) or with the median for the feature (as may be appropriate for multivariate analysis). (Note that the median feature-intensity is computed for the samples *before* variable-range filters are applied.)
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
820
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
821 -----------------------------------------------------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
822
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
823 ----------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
824 WORKING EXAMPLES
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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825 ----------------
2
23c6d271def9 planemo upload
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diff changeset
826
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
827 -----------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
828 Input Files
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
829 -----------
2
23c6d271def9 planemo upload
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diff changeset
830
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
831 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
832 | Input File URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
833 +======================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
834 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_dataMatrix.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
835 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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836 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_sampleMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
837 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
838 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_variableMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
839 +------------------------------------------------------------------------------------------------------------------------------------------------------+
2
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diff changeset
840
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
841 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
842 Running Without Range-Filtering
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
843 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
844
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
845 This example retains only samples whose 'gender' attribute is 'M'.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
846
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
847 **Input parameters**
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
848
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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849 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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850 | Input Parameter | Value |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
851 +=============================================+===============================+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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852 | Column that names the sample-class | gender |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
853 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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854 | Names of sample-classes | M |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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855 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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856 | Use 'wild-cards' or 'regular expressions' | wild-cards |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
857 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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858 | Exclude/include named classes | filter-in |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
859 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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860 | Variable range-filters | (Leave this field empty.) |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
861 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
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862 | Data transforamtion | none |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
863 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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864 | Missing-value imputation | center |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
865 +---------------------------------------------+-------------------------------+
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
866 | Sample-sort column | sampleMetadata |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
867 +---------------------------------------------+-------------------------------+
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
868 | Feature-sort column | variableMetadata |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
869 +---------------------------------------------+-------------------------------+
2
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diff changeset
870
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
871 **Expected outputs**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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872
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
873 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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874 | Expected Output | Download from URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
875 +===================+=================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
876 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_dataMatrix.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
877 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
878 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_sampleMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
879 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
880 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_variableMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
881 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
882
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
883 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
884 Running With Range-Filtering
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
885 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
886
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
887 This example retains only features whose mz is greater than 200, whose rt is less than 800, and whose maximum intensity across all samples is 2,000,000.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
888 This example retains all samples (except those having zero variance for all feature), although it would be possible to filter on samples as well.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
889
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
890 **Input parameters**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
891
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
892 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
893 | Input Parameter | Value |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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894 +=============================================+===================================+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
895 | Column that names the sample-class | sampleMetadata |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
896 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
897 | Names of sample-classes | HU_13[48] |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
898 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
899 | Use 'wild-cards' or 'regular expressions' | regular-expressions |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
900 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
901 | Exclude/include named classes | filter-out |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
902 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
903 | Variable range-filters | FEATMAX:20.93157:,mz:200:,rt::800 |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
904 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
905 | Data transforamtion | log2 |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
906 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
907 | Missing-value imputation | zero |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
908 +---------------------------------------------+-----------------------------------+
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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parents: 12
diff changeset
909 | Sample-sort column | sampleMetadata |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
910 +---------------------------------------------+-----------------------------------+
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
911 | Feature-sort column | variableMetadata |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
912 +---------------------------------------------+-----------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
913
2
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diff changeset
914 **Expected outputs**
23c6d271def9 planemo upload
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diff changeset
915
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
916 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
917 | Expected Output | Download from URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
918 +===================+===================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
919 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
920 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
921 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
922 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
923 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
924 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
925 ]]></help>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
926 <citations>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
927 <!-- Giacomoni_2014 W4m 2.5 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
928 <citation type="doi">10.1093/bioinformatics/btu813</citation>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
929 <!-- Guitton_2017 W4m 3.0 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
930 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
931 <!-- Kuhl_2012 CAMERA -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
932 <citation type="doi">10.1021/ac202450g</citation>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
933 <!-- Smith_2006 XCMS -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
934 <citation type="doi">10.1021/ac051437y</citation>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
935 <!-- Thevenot_2015 Urinary metabolome statistics -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
936 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
937 </citations>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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938 <!--
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
939 vim:noet:sw=4:ts=4
3
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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940 --> </tool>