Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 12:38f509903a0b draft

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"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
author eschen42
date Tue, 01 Oct 2019 16:57:58 -0400
parents 9f5c0e23c205
children c18040b6e8b9
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38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.13">
10
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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>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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6 <requirement type="package" version="1.1_5">r-batch</requirement>
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7 <requirement type="package" version="0.98.13">w4mclassfilter</requirement>
10
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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'
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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13 sampleMetadata_in '$sampleMetadata_in'
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14 variableMetadata_in '$variableMetadata_in'
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15 sampleclassNames '$sampleclassNames'
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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16 inclusive '$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 ]]></command>
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27 <inputs>
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28 <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"
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29 help="variables &#10006; samples" />
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30 <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data"
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31 help="sample metadata, one row per sample" />
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32 <param name="variableMetadata_in" format="tabular" label="Variable metadata file" type="data"
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33 help="variable metadata, one row per variable" />
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34 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class"
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35 help="name of the column in sample metadata that has the values to be tested against the 'Names of sample-classes' input parameter - defaults to 'class'">
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36 <sanitizer>
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37 <valid initial="string.letters">
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38 <add preset="string.digits"/>
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39 <add value="&#46;" /> <!-- dot, period -->
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40 <add value="&#95;" /> <!-- underscore -->
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41 </valid>
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42 </sanitizer>
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43 </param>
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44 <param name="sampleclassNames" label="Names of sample-classes" type="text" value = ""
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45 help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names">
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46 <sanitizer>
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47 <valid initial="string.letters">
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48 <add preset="string.digits"/>
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49 <add value="&#123;" /> <!-- l-cube, left-curly-bracket -->
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50 <add value="&#124;" /> <!-- pipe -->
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51 <add value="&#125;" /> <!-- r-cube, right-curly-bracket -->
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52 <add value="&#36;" /> <!-- dollar, dollar-sign -->
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53 <add value="&#40;" /> <!-- left-paren -->
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54 <add value="&#41;" /> <!-- right-paren -->
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55 <add value="&#42;" /> <!-- splat, asterisk -->
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56 <add value="&#43;" /> <!-- plus -->
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57 <add value="&#45;" /> <!-- dash, hyphen -->
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58 <add value="&#44;" /> <!-- comma -->
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59 <add value="&#46;" /> <!-- dot, period -->
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60 <add value="&#58;" /> <!-- colon -->
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61 <add value="&#59;" /> <!-- semi, semicolon -->
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62 <add value="&#63;" /> <!-- what, question mark -->
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63 <add value="&#91;" /> <!-- l-squib, left-squre-bracket -->
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64 <add value="&#92;" /> <!-- whack, backslash -->
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65 <add value="&#93;" /> <!-- r-squib, right-squre-bracket -->
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66 <add value="&#94;" /> <!-- hat, caret -->
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67 <add value="&#95;" /> <!-- underscore -->
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68 </valid>
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69 </sanitizer>
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70 </param>
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71 <param name="wildcards" label="Use 'wild cards' or 'regular expressions'" type="select"
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72 help="'wild-cards' (the default) - use '*' and '?' to match class names; 'regular-expressions' - use regular expressions to match class names">
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73 <option value="TRUE" selected="true">wild-cards</option>
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74 <option value="FALSE">regular-expressions</option>
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75 </param>
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76 <param name="inclusive" label="Exclude/include named classes" type="select"
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77 help="'filter-out' (the default) - exclude only the named sample-classes; 'filter-in' - include only the named sample-classes">
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78 <option value="TRUE">filter-in</option>
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79 <option value="FALSE" selected="true">filter-out</option>
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80 </param>
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81 <param name="variableRangeFilter" label="Variable-range filters" type="text" value = ""
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82 help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)">
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83 <sanitizer>
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84 <valid initial="string.letters">
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85 <add preset="string.digits"/>
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86 <add value="&#44;" /> <!-- comma -->
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87 <add value="&#46;" /> <!-- dot, period -->
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88 <add value="&#58;" /> <!-- colon -->
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89 <add value="&#95;" /> <!-- underscore -->
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90 </valid>
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91 </sanitizer>
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92 </param>
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93 <param name="transformation" label="Data-transformation" type="select"
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94 help="'none' (the default) - do not transform data; 'log2' - log base 2 of data; 'log10' - log base 10 of data; in all cases, negative and missing values are imputed to zero">
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95 <option value="none" selected="true">none</option>
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96 <option value="log2">log2</option>
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97 <option value="log10">log10</option>
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98 </param>
12
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99 <param name="imputation" label="Imputation of missing values" type="select"
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100 help="'zero' (the default) - replace missing values with zero; 'center' - replace missing values with feature-median; 'none' - perform no imputation">
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101 <option value="zero" selected="true">zero</option>
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102 <option value="center">center</option>
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103 <option value="none">none</option>
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104 </param>
10
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105 </inputs>
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106 <outputs>
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107 <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>
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108 <data name="sampleMetadata_out" format="tabular" label="${sampleMetadata_in.name}.subset" ></data>
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109 <data name="variableMetadata_out" format="tabular" label="${variableMetadata_in.name}.subset" ></data>
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110 </outputs>
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111 <tests>
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112 <!-- test 1 -->
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113 <test>
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114 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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115 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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116 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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117 <param name="classnameColumn" value="gender"/>
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118 <param name="sampleclassNames" value="M"/>
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119 <param name="wildcards" value="FALSE"/>
12
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120 <param name="inclusive" value="TRUE"/>
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121 <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/>
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122 <param name="transformation" value="none"/>
10
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123 <output name="dataMatrix_out">
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124 <assert_contents>
12
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125 <has_text text="747080" />
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126 <not_has_text text="13420742" />
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127 <not_has_text text="47259" />
10
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128 </assert_contents>
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129 </output>
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130 <output name="sampleMetadata_out">
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131 <assert_contents>
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132 <has_text text="HU_017" />
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133 <has_text text="HU_034" />
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134 <has_text text="HU_078" />
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135 <has_text text="HU_091" />
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136 <has_text text="HU_093" />
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137 <has_text text="HU_099" />
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138 <has_text text="HU_130" />
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139 <has_text text="HU_134" />
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140 <has_text text="HU_138" />
10
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141 <not_has_text text="HU_028" />
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142 <not_has_text text="HU_051" />
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143 <not_has_text text="HU_060" />
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144 <not_has_text text="HU_110" />
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145 <not_has_text text="HU_149" />
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146 <not_has_text text="HU_152" />
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147 <not_has_text text="HU_175" />
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148 <not_has_text text="HU_178" />
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149 <not_has_text text="HU_185" />
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150 <not_has_text text="HU_204" />
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151 <not_has_text text="HU_208" />
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152 </assert_contents>
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153 </output>
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154 <output name="variableMetadata_out">
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155 <assert_contents>
12
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156 <has_text text="HMDB00208" />
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157 <has_text text="HMDB01032" />
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158 <has_text text="HMDB01101.1" />
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159 <has_text text="HMDB13189" />
10
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160 <not_has_text text="HMDB00191" />
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161 <not_has_text text="HMDB00251" />
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162 <not_has_text text="HMDB00299" />
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163 <not_has_text text="HMDB00512" />
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164 <not_has_text text="HMDB00518" />
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165 <not_has_text text="HMDB00715" />
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166 <not_has_text text="HMDB00822" />
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167 <not_has_text text="HMDB03193" />
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168 <not_has_text text="HMDB04824" />
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169 <not_has_text text="HMDB10348" />
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170 <not_has_text text="HMDB59717" />
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171 </assert_contents>
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172 </output>
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173 </test>
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174 <!-- test 2 -->
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175 <test>
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176 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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177 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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178 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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179 <!-- test that hyphens in regular expressions work -->
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180 <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/>
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181 <param name="inclusive" value="TRUE"/>
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182 <param name="wildcards" value="FALSE"/>
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183 <param name="classnameColumn" value="sampleMetadata"/>
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184 <!-- test that variableRangeFilter works with tranformation -->
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185 <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
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186 <param name="transformation" value="log10"/>
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187 <param name="imputation" value="zero"/>
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188 <output name="dataMatrix_out" md5="5644d2ea01d072ee1d0c40e29e9d0089">
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189 <assert_contents>
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190 <has_text text="5.8733671" />
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191 </assert_contents>
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192 </output>
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193 <output name="sampleMetadata_out">
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194 <assert_contents>
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195 <has_text text="HU_017" />
10
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196 <has_text text="HU_028" />
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197 <has_text text="HU_034" />
10
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198 <has_text text="HU_051" />
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199 <has_text text="HU_060" />
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200 <has_text text="HU_078" />
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201 <has_text text="HU_091" />
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202 <has_text text="HU_093" />
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203 <has_text text="HU_099" />
10
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204 <has_text text="HU_110" />
12
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205 <has_text text="HU_130" />
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206 <has_text text="HU_134" />
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207 <has_text text="HU_138" />
10
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208 <has_text text="HU_149" />
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209 <has_text text="HU_152" />
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210 <has_text text="HU_175" />
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211 <has_text text="HU_178" />
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212 <has_text text="HU_185" />
12
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213 <has_text text="HU_208" />
10
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214 <not_has_text text="HU_204" />
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215 </assert_contents>
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216 </output>
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217 <output name="variableMetadata_out">
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218 <assert_contents>
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219 <has_text text="HMDB00191" />
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220 <has_text text="HMDB00208" />
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221 <has_text text="HMDB01032" />
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222 <has_text text="HMDB01101.1" />
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223 <has_text text="HMDB13189" />
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224 <not_has_text text="HMDB00251" />
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225 <not_has_text text="HMDB00299" />
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226 <not_has_text text="HMDB00512" />
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227 <not_has_text text="HMDB00518" />
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228 <not_has_text text="HMDB00715" />
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229 <not_has_text text="HMDB00822" />
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230 <not_has_text text="HMDB03193" />
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231 <not_has_text text="HMDB04824" />
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232 <not_has_text text="HMDB10348" />
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233 <not_has_text text="HMDB59717" />
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234 </assert_contents>
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235 </output>
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236 </test>
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237 <!-- test 3 -->
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238 <test>
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239 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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240 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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241 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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242 <param name="classnameColumn" value="gender"/>
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243 <param name="sampleclassNames" value="M"/>
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244 <param name="inclusive" value="TRUE"/>
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245 <param name="transformation" value="none"/>
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246 <output name="dataMatrix_out">
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247 <assert_contents>
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248 <not_has_text text="HU_028" />
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249 <not_has_text text="HU_051" />
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250 <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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251 <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
252 <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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253 <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
254 <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
255 <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
256 <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
257 <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
258 <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
259 <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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260 <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
261 <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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262 <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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263 <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
264 <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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265 <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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266 <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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267 <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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268 <has_text text="HMDB03193" />
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269 <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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270 <has_text text="HMDB01101" />
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271 <has_text text="HMDB01101.1" />
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272 <has_text text="HMDB10348" />
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273 <has_text text="HMDB59717" />
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274 <has_text text="HMDB13189" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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275 <has_text text="HMDB00299" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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276 <has_text text="HMDB00191" />
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277 <has_text text="HMDB00518" />
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278 <has_text text="HMDB00715" />
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279 <has_text text="HMDB01032" />
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280 <has_text text="HMDB00208" />
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281 <has_text text="HMDB04824" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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282 <has_text text="HMDB00512" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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283 <has_text text="HMDB00251" />
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284 </assert_contents>
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285 </output>
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286 </test>
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287 <!-- test 4 -->
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288 <test>
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289 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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290 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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291 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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292 <param name="classnameColumn" value="gender"/>
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293 <param name="sampleclassNames" value="*"/>
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294 <param name="wildcards" value="TRUE"/>
12
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295 <param name="inclusive" value="TRUE"/>
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296 <param name="imputation" value="zero"/>
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297 <output name="dataMatrix_out" md5="b2eac4946d3803a07606286b50451af4">
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298 <assert_contents>
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299 <not_has_text text="NA" />
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300 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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301 </output>
10
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302 <output name="sampleMetadata_out">
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303 <assert_contents>
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304 <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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305 <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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306 <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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307 <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
308 <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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309 <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
310 <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
311 <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
312 <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
313 <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
314 <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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315 <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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316 <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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317 <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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318 <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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319 <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
320 <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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321 <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
322 <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
323 <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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324 </assert_contents>
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325 </output>
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326 </test>
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327 <!-- test 5 -->
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328 <test>
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329 <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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330 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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331 <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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332 <param name="classnameColumn" value="gender"/>
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333 <param name="sampleclassNames" value="M"/>
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334 <param name="wildcards" value="FALSE"/>
12
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335 <param name="inclusive" value="TRUE"/>
10
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336 <output name="sampleMetadata_out">
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337 <assert_contents>
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diff changeset
338 <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
339 <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
340 <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
341 <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
342 <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
343 <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
344 <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
345 <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
346 <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
347 <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
348 <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
349 <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
350 <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
351 <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
352 <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
353 <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
354 <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
355 <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
356 <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
357 <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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358 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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359 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
360 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
361 <!-- test 6 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
362 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
363 <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
364 <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
365 <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
366 <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
367 <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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368 <param name="wildcards" value="FALSE"/>
12
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diff changeset
369 <param name="inclusive" value="TRUE"/>
10
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diff changeset
370 <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
371 <assert_contents>
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="HMDB03193" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
373 <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
374 <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
375 <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
376 <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
377 <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
378 <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
379 <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
380 <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
381 <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
382 <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
383 <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
384 <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
385 <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
386 <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
387 <has_text text="HMDB00251" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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388 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
389 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
390 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
391 <!-- test 7 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
392 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
393 <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
394 <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
395 <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
396 <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
397 <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
398 <param name="wildcards" value="FALSE"/>
12
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diff changeset
399 <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
400 <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
401 <assert_contents>
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="HMDB03193" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
403 <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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parents: 9
diff changeset
404 <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
405 <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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parents: 9
diff changeset
406 <has_text text="HMDB10348" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
407 <has_text text="HMDB59717" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
408 <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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parents: 9
diff changeset
409 <has_text text="HMDB00299" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
410 <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
411 <has_text text="HMDB00518" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
412 <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
413 <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
414 <has_text text="HMDB00208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
415 <has_text text="HMDB04824" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
416 <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
417 <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
418 </assert_contents>
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diff changeset
419 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
420 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
421 <!-- test 8 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
422 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
423 <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
424 <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
425 <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
426 <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
427 <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
428 <param name="wildcards" value="FALSE"/>
12
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diff changeset
429 <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
430 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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431 <assert_contents>
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="HU_028" />
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="HU_051" />
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="HU_060" />
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="HU_110" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
436 <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
437 <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
438 <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
439 <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
440 <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
441 <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
442 <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
443 <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
444 <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
445 <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
446 <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
447 <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
448 <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
449 <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
450 <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
451 <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
452 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
453 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
454 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
455 <!-- test 9 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
456 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
457 <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
458 <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
459 <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
460 <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
461 <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
462 <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
463 <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
464 <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
465 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
466 <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
467 <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
468 <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
469 <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
470 <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
471 <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
472 <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
473 <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
474 <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
475 <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
476 <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
477 <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
478 <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
479 <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
480 <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
481 <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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parents: 9
diff changeset
482 <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
483 <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
484 <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
485 <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
486 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
487 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
488 </test>
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
489 <!-- 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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diff changeset
490 <test>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
491 <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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diff changeset
492 <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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diff changeset
493 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
494 <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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diff changeset
495 <param name="sampleclassNames" value="*"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
496 <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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diff changeset
497 <param name="inclusive" value="TRUE"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
498 <param name="imputation" value="none"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
499 <output name="dataMatrix_out" md5="cc9ab8bdb70b68b43b19b7327d285166">
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
500 <assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
501 <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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diff changeset
502 <has_text text="NA" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
503 <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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diff changeset
504 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
505 </output>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
506 <output name="sampleMetadata_out">
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
507 <assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
508 <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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parents: 11
diff changeset
509 <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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diff changeset
510 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
511 </output>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
512 </test>
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513 <!-- test 11 - extends test4 with center imputation rather than zero imputation -->
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514 <test>
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515 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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516 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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517 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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518 <param name="classnameColumn" value="gender"/>
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519 <param name="sampleclassNames" value="*"/>
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520 <param name="wildcards" value="TRUE"/>
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521 <param name="inclusive" value="TRUE"/>
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522 <param name="imputation" value="center"/>
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523 <output name="dataMatrix_out" md5="75a4802bb8887709e4d4dec8c2c3d3cf">
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524 <assert_contents>
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525 <not_has_text text="HU_204" />
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526 <not_has_text text="NA" />
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527 <has_text text="HU_028" />
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528 </assert_contents>
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529 </output>
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530 <output name="sampleMetadata_out">
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531 <assert_contents>
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532 <not_has_text text="HU_204" />
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533 <has_text text="HU_028" />
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534 </assert_contents>
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535 </output>
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536 </test>
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537 </tests>
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538 <help><![CDATA[
0
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539
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540
5
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541 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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542
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543 --------------------------------------------------------------------------
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544
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545
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546 **R package**
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547
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548 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).
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549
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550 -----------------------------------------------------------------------------------------------------------------------------------------
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551
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552
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553 **Tool updates**
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554
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555 See the **NEWS** section at the bottom of this page
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556
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557 ---------------------------------------------------
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558
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559 ===========================================================
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560 "W4m Data Subset" - Filter Workflow4Metabolomics data files
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561 ===========================================================
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562
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563 ----------
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564 Motivation
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565 ----------
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566
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567 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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568 (If the MS protocol includes fragmentation, several features may result for each chemical.)
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569 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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570 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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571
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572 The chromatographic retention-time for a chemical can vary from one chromatography run to the next.
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573 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.
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574 Features may be better aligned if pooled samples and blanks are included.
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575
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576 Multivariate statistical techniques may be used to discover clusters of similar samples (Th]]>&#233;<![CDATA[venot *et al.*, 2015).
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577 However, once retention-time alignment of features has been achieved among samples in GC-MS and LC-MS datasets:
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578
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579 - The presence of pools and blanks may confound identification and separation of clusters.
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580 - Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance.
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581
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582 -----------
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583 Description
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584 -----------
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585
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586 The **W4m Data Subset** tool **selects subsets of samples, features, or data values** for further analysis.
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587
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588 - 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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589 - The tool produces the same trio of output datasets, modified as follows.
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590
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591 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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592
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593 - Samples may be eliminated by filtering on a designated “sample class” column in sampleMetadata.
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594 - Features may be eliminated by specifying minimum or maximum value (or both) allowable in columns of variableMetadata.
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595 - 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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596
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597 This tool also performs several operations to address several data issues that may impede downstream statistical analysis:
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598
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599 - Samples that are missing from either sampleMetadata or dataMatrix are eliminated.
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600 - Features that are missing from either variableMetadata or dataMatrix are eliminated.
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601 - Features and samples that have zero variance are eliminated.
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602 - Samples and features are sorted alphabetically in rows and columns of dataMatrix and in rows of variableMetadata and sampleMetadata.
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603 - The names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata".
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604 - If desired, the values in the dataMatrix may be log-transformed.
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605 - If desired, each missing value in dataMatrix is replaced with zero or the median value observed for the corresponding feature.
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606
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607 This tool may be applied several times sequentially, which may be useful for:
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608
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609 - analyzing subsets of samples for progressively smaller sets of treatment-levels, or
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610 - choosing subsets of samples based on criteria in several columns of the sampleMetadata table.
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611
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612 -----------------
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613 Workflow Position
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614 -----------------
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615
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616 This tool can be used at any point downstream of Preprocessing.
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617
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618 - Possible upstream tool categories: Preprocessing, Quality Control, Statistical Analysis, Filter and Sort
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619 - Possible downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
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620
0
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621 -----------
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622 Input files
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623 -----------
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624
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625 +---------------------------+------------+
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626 | File | Format |
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627 +===========================+============+
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628 | Data matrix | tabular |
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629 +---------------------------+------------+
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630 | Sample metadata | tabular |
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631 +---------------------------+------------+
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632 | Variable metadata | tabular |
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633 +---------------------------+------------+
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634
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635
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636 ----------
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637 Parameters
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638 ----------
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639
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640 Data matrix file
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641 | variable x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical, respectively, to the rownames of the sample metadata file and variable metadata file
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642 |
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643
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644 Sample metadata file
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645 | 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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646 |
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647
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648 Variable metadata file
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649 | 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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650 |
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651
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652 Column that names the sample-class (default = '``class``')
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653 | 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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654 |
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655
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656 Names of sample-classes (default = no names)
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657 | comma-separated names (or regular expressions to match names) of sample-classes to include or exclude
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658 |
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659
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660 'Wild cards' or 'regular expressions' (default = '``wild-cards``')
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661 | '``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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662 | '``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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663 |
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664
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665 Exclude/include named classes (default = '``filter-out``')
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666 | '``filter-in``' - include only the named sample-classes
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667 | '``filter-out``' - exclude only the named sample-classes
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668 |
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669
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670 Variable-range filters (default = no filters)
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671 | comma-separated names of variable-range filters (see the 'Variable-range filters' section below)
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672 |
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673
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674 Data-transformation (default = '``none``')
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675 | '``none``' - Do not transform data matrix values.
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676 | '``log2``' - Take the log base 2 of the values in the data matrix.
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677 | '``log10``' - Take the log base 10 of the values in the data matrix.
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678 |
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679
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680 Data-imputation (default = '``zero``')
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681 | '``none``' - Do not impute data matrix values.
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682 | '``zero``' - Negative and missing values are imputed to zero.
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683 | '``center``' - For each feature, negative and missing values are imputed to the median of other values.
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684 |
0
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685
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686
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687 ------------
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688 Output files
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689 ------------
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690
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691 sampleMetadata
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692 | (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)
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693 |
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694
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695 variableMetadata
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696 | (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)
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697 |
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698
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699 dataMatrix
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700 | (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
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701 |
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702
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703
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704 -----------------------------------------
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705 'Wild card' patterns to match class-names
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706 -----------------------------------------
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707
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708 W4m Data Subset supports use of R "wild card" patterns to select class-names.
4
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diff changeset
709
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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710 - use '``?``' to match a single character
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711 - 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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712 - the entire pattern must match the sample name
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diff changeset
713
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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714 For example
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
715
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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716 - '``??.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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717 - '``*.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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diff changeset
718 - '``*.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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diff changeset
719
8
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diff changeset
720 --------------------------------------------------
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
721 '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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722 --------------------------------------------------
4
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723
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
724 W4m Data Subset supports use of R "regular expression" patterns to select class-names.
4
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diff changeset
725
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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726 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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727 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
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728
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diff changeset
729 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
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diff changeset
730
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diff changeset
731 - '``^``' matches the beginning of a class-name
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732 - '``$``' matches the end of a class-name
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733 - '``.``' outside of square brackets matches a single character
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734 - '``*``' matches character specified immediately before zero or more times
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735 - square brackets specify a set of characters to be matched.
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diff changeset
736
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diff changeset
737 Within square brackets
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diff changeset
738
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739 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
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740 - '``-``' is used to specify ranges of characters
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diff changeset
741
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
742 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**
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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 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
745
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diff changeset
746 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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747 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
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diff changeset
748 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
749 - The regular expression '``^[a-z][a-z][0-9]$``' 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
750
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751 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
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diff changeset
752
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diff changeset
753 - '``^[A-Z][A-Z][0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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754 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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755 - '``^[A-Z][0-9]*``' - MATCHES '``**^A** B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
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756 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
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757 - '``^[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
758 - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
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diff changeset
759
6
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760 ----------------------
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diff changeset
761 Variable-range filters
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762 ----------------------
4
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diff changeset
763
6
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diff changeset
764 An array of range-specification strings may be supplied in the `variableRangeFilter`
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diff changeset
765 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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766 of `variableMetadata` that fall within the specified ranges will be retained
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767 in the output. Each range is a string of three colon-separated values (e.g., "mz:200:800") in the
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diff changeset
768 following order:
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
769
11
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770 - 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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771 - 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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772 - the **maximum allowed value**, e.g., '800'.
6
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diff changeset
773
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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774 Note for the range specification strings:
6
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diff changeset
775
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776 - **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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777 - **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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diff changeset
778
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779 - Note, however, that when the "maximum" is greater than the "minimum" for the FEATMAX range specification, then the specification is ignored.
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780
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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781 ----------------------------------
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
782 Data transformation and imputation
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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783 ----------------------------------
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
784
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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785 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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diff changeset
786
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
787 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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diff changeset
788
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
789 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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diff changeset
790
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
791 -----------------------------------------------------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
792
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
793 ----------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
794 WORKING EXAMPLES
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
795 ----------------
2
23c6d271def9 planemo upload
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parents: 0
diff changeset
796
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
797 -----------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
798 Input Files
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
799 -----------
2
23c6d271def9 planemo upload
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parents: 0
diff changeset
800
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
801 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
802 | Input File URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
803 +======================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
804 | 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
eschen42
parents: 9
diff changeset
805 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
806 | 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
eschen42
parents: 9
diff changeset
807 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
808 | 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
eschen42
parents: 9
diff changeset
809 +------------------------------------------------------------------------------------------------------------------------------------------------------+
2
23c6d271def9 planemo upload
eschen42
parents: 0
diff changeset
810
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
811 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
812 Running Without Range-Filtering
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
813 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
814
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
815 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
eschen42
parents: 5
diff changeset
816
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
817 **Input parameters**
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
eschen42
parents:
diff changeset
818
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
819 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
820 | Input Parameter | Value |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
821 +=============================================+===============================+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
822 | Column that names the sample-class | gender |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
823 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
824 | Names of sample-classes | M |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
825 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
826 | Use 'wild-cards' or 'regular expressions' | wild-cards |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
827 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
828 | Exclude/include named classes | filter-in |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
829 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
830 | Variable range-filters | (Leave this field empty.) |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
831 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
832 | Data transforamtion | none |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
833 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
834 | Missing-value imputation | center |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
835 +---------------------------------------------+-------------------------------+
2
23c6d271def9 planemo upload
eschen42
parents: 0
diff changeset
836
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
837 **Expected outputs**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
838
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
839 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
840 | Expected Output | Download from URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
841 +===================+=================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
842 | 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
eschen42
parents: 9
diff changeset
843 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
844 | 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
eschen42
parents: 9
diff changeset
845 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
846 | 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
eschen42
parents: 9
diff changeset
847 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
848
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
849 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
850 Running With Range-Filtering
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
851 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
852
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
853 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
eschen42
parents: 5
diff changeset
854 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
eschen42
parents: 5
diff changeset
855
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
856 **Input parameters**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
857
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
858 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
859 | Input Parameter | Value |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
860 +=============================================+===================================+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
861 | Column that names the sample-class | sampleMetadata |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
862 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
863 | Names of sample-classes | HU_13[48] |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
864 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
865 | Use 'wild-cards' or 'regular expressions' | regular-expressions |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
866 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
867 | Exclude/include named classes | filter-out |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
868 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
869 | 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"
eschen42
parents: 11
diff changeset
870 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
871 | Data transforamtion | log2 |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
872 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
873 | Missing-value imputation | zero |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
874 +---------------------------------------------+-----------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
875
2
23c6d271def9 planemo upload
eschen42
parents: 0
diff changeset
876 **Expected outputs**
23c6d271def9 planemo upload
eschen42
parents: 0
diff changeset
877
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
878 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
879 | Expected Output | Download from URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
880 +===================+===================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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881 | 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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882 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
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883 | 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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884 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
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885 | 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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886 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
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887 ]]></help>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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888 <citations>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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889 <!-- 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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890 <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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891 <!-- Guitton_2017 W4m 3.0 -->
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892 <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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893 <!-- Kuhl_2012 CAMERA -->
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894 <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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895 <!-- Smith_2006 XCMS -->
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896 <citation type="doi">10.1021/ac051437y</citation>
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897 <!-- Thevenot_2015 Urinary metabolome statistics -->
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898 <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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899 </citations>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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900 <!--
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901 vim:noet:sw=4:ts=4
3
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902 --> </tool>