Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 7:582a8a42a93b draft

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planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
author eschen42
date Mon, 29 Jan 2018 21:20:07 -0500
parents 38ccf6722d54
children d5cf23369d12
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1 <tool id="w4mclassfilter" name="Sample_Subset" version="0.98.7">
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2 <!-- this file is utf-8, not ASCII, because it contains the character é -->
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3 <description>Filter W4M data by sample class</description>
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4
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5 <requirements>
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6 <!-- <requirement type="package" version="6.2">readline</requirement> -->
6
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7 <requirement type="package" version="3.4.1">r-base</requirement>
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8 <requirement type="package" version="1.1_4">r-batch</requirement>
7
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9 <requirement type="package" version="0.98.7">w4mclassfilter</requirement>
0
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10 </requirements>
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11
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12 <stdio>
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13 <exit_code range="1:" level="fatal" />
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14 </stdio>
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15
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16
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17 <command detect_errors="aggressive"><![CDATA[
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18 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
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19 dataMatrix_in '$dataMatrix_in'
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20 sampleMetadata_in '$sampleMetadata_in'
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21 variableMetadata_in '$variableMetadata_in'
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22 sampleclassNames '$sampleclassNames'
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23 inclusive '$inclusive'
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24 wildcards '$wildcards'
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25 classnameColumn '$classnameColumn'
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26 samplenameColumn '$samplenameColumn'
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27 variable_range_filter '$variableRangeFilter'
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28 dataMatrix_out '$dataMatrix_out'
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29 sampleMetadata_out '$sampleMetadata_out'
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30 variableMetadata_out '$variableMetadata_out'
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31 ]]></command>
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32
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33 <inputs>
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34 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
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35 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
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36 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
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37 <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in the sample metadata file that has the name of the sample - defaults to 'sampleMetadata'" />
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38 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the 'classes' input parameter - defaults to 'class'" />
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39 <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names (or comma-less regular expressions to match names) of sample-classes to filter in or out; defaults to no names">
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40 <sanitizer>
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41 <valid initial="string.letters">
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42 <add preset="string.digits"/>
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43 <add value="&#36;" /> <!-- dollar, dollar-sign -->
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44 <add value="&#40;" /> <!-- left-paren -->
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45 <add value="&#41;" /> <!-- right-paren -->
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46 <add value="&#42;" /> <!-- splat, asterisk -->
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47 <add value="&#43;" /> <!-- plus -->
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48 <add value="&#44;" /> <!-- comma -->
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49 <add value="&#46;" /> <!-- dot, period -->
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50 <add value="&#58;" /> <!-- colon -->
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51 <add value="&#59;" /> <!-- semi, semicolon -->
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52 <add value="&#63;" /> <!-- what, question mark -->
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53 <add value="&#91;" /> <!-- l-squib, left-squre-bracket -->
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54 <add value="&#92;" /> <!-- whack, backslash -->
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55 <add value="&#93;" /> <!-- r-squib, right-squre-bracket -->
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56 <add value="&#94;" /> <!-- hat, caret -->
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57 <add value="&#123;" /> <!-- l-cube, left-curly-bracket -->
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58 <add value="&#124;" /> <!-- pipe -->
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59 <add value="&#125;" /> <!-- r-cube, right-curly-bracket -->
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60 </valid>
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61 </sanitizer>
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62 </param>
5
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63
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64 <param name="wildcards" label="Use wild-cards or regular-expressions" type="select" help="wild-cards (the default) - use '*' and '?' to match class names; regular-expressions - use comma-less regular expressions to match class names">
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65 <option value="TRUE" selected="true">wild-cards</option>
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66 <option value="FALSE">regular-expressions</option>
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67 </param>
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68 <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes">
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69 <option value="TRUE">filter-in</option>
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70 <option value="FALSE" selected="true">filter-out</option>
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71 </param>
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72
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73 <param name="variableRangeFilter" label="Variable range-filters" type="text" value = "" help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)">
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74 <sanitizer>
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75 <valid initial="string.letters">
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76 <add preset="string.digits"/>
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77 <add value="&#44;" /> <!-- comma -->
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78 <add value="&#58;" /> <!-- colon -->
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79 <add value="&#46;" /> <!-- dot, period -->
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80 </valid>
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81 </sanitizer>
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82 </param>
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83
0
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84 </inputs>
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85 <outputs>
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86 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
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87 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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88 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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89 </outputs>
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90
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91 <tests>
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92 <test>
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93 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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94 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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95 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
6
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96 <param name="classnameColumn" value="class"/>
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97 <param name="sampleclassNames" value=""/>
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98 <param name="wildcards" value="FALSE"/>
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99 <param name="samplenameColumn" value="sampleMetadata"/>
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100 <param name="inclusive" value="filter-out"/>
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101 <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/>
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102 <output name="sampleMetadata_out">
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103 <assert_contents>
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104 <has_text text="HU_028" />
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105 <has_text text="HU_051" />
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106 <has_text text="HU_060" />
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107 <has_text text="HU_110" />
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108 <has_text text="HU_149" />
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109 <has_text text="HU_152" />
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110 <has_text text="HU_175" />
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111 <has_text text="HU_178" />
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112 <has_text text="HU_185" />
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113 <not_has_text text="HU_204" />
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114 <has_text text="HU_208" />
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115 <has_text text="HU_017" />
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116 <has_text text="HU_034" />
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117 <has_text text="HU_078" />
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118 <has_text text="HU_091" />
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119 <has_text text="HU_093" />
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120 <has_text text="HU_099" />
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121 <has_text text="HU_130" />
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122 <has_text text="HU_134" />
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123 <has_text text="HU_138" />
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124 </assert_contents>
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125 </output>
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126 <output name="variableMetadata_out">
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127 <assert_contents>
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128 <has_text text="HMDB00191" />
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129 <has_text text="HMDB00208" />
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130 <not_has_text text="HMDB00251" />
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131 <not_has_text text="HMDB00299" />
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132 <not_has_text text="HMDB00512" />
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133 <not_has_text text="HMDB00518" />
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134 <not_has_text text="HMDB00715" />
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135 <not_has_text text="HMDB00822" />
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136 <has_text text="HMDB01032" />
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137 <has_text text="HMDB01101.1" />
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138 <not_has_text text="HMDB03193" />
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139 <not_has_text text="HMDB04824" />
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140 <not_has_text text="HMDB10348" />
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141 <has_text text="HMDB13189" />
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142 <not_has_text text="HMDB59717" />
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143 </assert_contents>
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144 </output>
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145 </test>
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146 <test>
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147 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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148 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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149 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
0
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150 <param name="classnameColumn" value="gender"/>
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151 <param name="sampleclassNames" value="M"/>
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152 <param name="samplenameColumn" value="sampleMetadata"/>
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153 <param name="inclusive" value="filter-in"/>
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154 <output name="dataMatrix_out">
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155 <assert_contents>
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156 <not_has_text text="HU_028" />
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157 <not_has_text text="HU_051" />
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158 <not_has_text text="HU_060" />
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159 <not_has_text text="HU_110" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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160 <not_has_text text="HU_149" />
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161 <not_has_text text="HU_152" />
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162 <not_has_text text="HU_175" />
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163 <not_has_text text="HU_178" />
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164 <not_has_text text="HU_185" />
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165 <not_has_text text="HU_204" />
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166 <not_has_text text="HU_208" />
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167 <has_text text="HU_017" />
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168 <has_text text="HU_034" />
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169 <has_text text="HU_078" />
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170 <has_text text="HU_091" />
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171 <has_text text="HU_093" />
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172 <has_text text="HU_099" />
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173 <has_text text="HU_130" />
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174 <has_text text="HU_134" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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175 <has_text text="HU_138" />
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176 <has_text text="HMDB03193" />
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177 <not_has_text text="HMDB00822" />
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178 <has_text text="HMDB01101" />
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179 <has_text text="HMDB01101.1" />
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180 <has_text text="HMDB10348" />
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181 <has_text text="HMDB59717" />
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182 <has_text text="HMDB13189" />
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183 <has_text text="HMDB00299" />
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184 <has_text text="HMDB00191" />
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185 <has_text text="HMDB00518" />
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186 <has_text text="HMDB00715" />
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187 <has_text text="HMDB01032" />
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188 <has_text text="HMDB00208" />
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189 <has_text text="HMDB04824" />
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190 <has_text text="HMDB00512" />
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191 <has_text text="HMDB00251" />
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192 </assert_contents>
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193 </output>
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194 </test>
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195 <test>
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196 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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197 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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198 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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199 <param name="classnameColumn" value="gender"/>
5
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200 <param name="sampleclassNames" value="*"/>
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201 <param name="wildcards" value="TRUE"/>
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202 <param name="samplenameColumn" value="sampleMetadata"/>
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203 <param name="inclusive" value="filter-in"/>
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204 <output name="sampleMetadata_out">
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205 <assert_contents>
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206 <not_has_text text="HU_204" />
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207 <has_text text="HU_028" />
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208 <has_text text="HU_051" />
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209 <has_text text="HU_060" />
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210 <has_text text="HU_110" />
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211 <has_text text="HU_149" />
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212 <has_text text="HU_152" />
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213 <has_text text="HU_175" />
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214 <has_text text="HU_178" />
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215 <has_text text="HU_185" />
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216 <has_text text="HU_208" />
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217 <has_text text="HU_017" />
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218 <has_text text="HU_034" />
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219 <has_text text="HU_078" />
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220 <has_text text="HU_091" />
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221 <has_text text="HU_093" />
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222 <has_text text="HU_099" />
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223 <has_text text="HU_130" />
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224 <has_text text="HU_134" />
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225 <has_text text="HU_138" />
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226 </assert_contents>
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227 </output>
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228 </test>
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229 <test>
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230 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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231 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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232 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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233 <param name="classnameColumn" value="gender"/>
0
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234 <param name="sampleclassNames" value="M"/>
5
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235 <param name="wildcards" value="FALSE"/>
0
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236 <param name="samplenameColumn" value="sampleMetadata"/>
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237 <param name="inclusive" value="filter-in"/>
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238 <output name="sampleMetadata_out">
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239 <assert_contents>
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240 <not_has_text text="HU_028" />
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241 <not_has_text text="HU_051" />
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242 <not_has_text text="HU_060" />
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243 <not_has_text text="HU_110" />
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244 <not_has_text text="HU_149" />
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245 <not_has_text text="HU_152" />
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246 <not_has_text text="HU_175" />
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247 <not_has_text text="HU_178" />
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248 <not_has_text text="HU_185" />
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249 <not_has_text text="HU_204" />
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250 <not_has_text text="HU_208" />
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251 <has_text text="HU_017" />
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252 <has_text text="HU_034" />
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253 <has_text text="HU_078" />
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254 <has_text text="HU_091" />
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255 <has_text text="HU_093" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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256 <has_text text="HU_099" />
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257 <has_text text="HU_130" />
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258 <has_text text="HU_134" />
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259 <has_text text="HU_138" />
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260 </assert_contents>
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261 </output>
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262 </test>
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263 <test>
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264 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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265 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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266 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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267 <param name="classnameColumn" value="gender"/>
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268 <param name="sampleclassNames" value="M"/>
5
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269 <param name="wildcards" value="FALSE"/>
0
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270 <param name="samplenameColumn" value="sampleMetadata"/>
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271 <param name="inclusive" value="filter-in"/>
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272 <output name="variableMetadata_out">
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273 <assert_contents>
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274 <has_text text="HMDB03193" />
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275 <not_has_text text="HMDB00822" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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276 <has_text text="HMDB01101" />
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277 <has_text text="HMDB01101.1" />
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278 <has_text text="HMDB10348" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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279 <has_text text="HMDB59717" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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280 <has_text text="HMDB13189" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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281 <has_text text="HMDB00299" />
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282 <has_text text="HMDB00191" />
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283 <has_text text="HMDB00518" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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284 <has_text text="HMDB00715" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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285 <has_text text="HMDB01032" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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286 <has_text text="HMDB00208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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287 <has_text text="HMDB04824" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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288 <has_text text="HMDB00512" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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289 <has_text text="HMDB00251" />
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290 </assert_contents>
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291 </output>
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292 </test>
4
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293 <test>
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294 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/>
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295 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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296 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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297 <param name="classnameColumn" value="gender"/>
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298 <param name="sampleclassNames" value="M"/>
5
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299 <param name="wildcards" value="FALSE"/>
4
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300 <param name="samplenameColumn" value="sampleMetadata"/>
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301 <param name="inclusive" value="filter-in"/>
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302 <output name="variableMetadata_out">
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303 <assert_contents>
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304 <has_text text="HMDB03193" />
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305 <not_has_text text="HMDB00822" />
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306 <has_text text="HMDB01101" />
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307 <has_text text="HMDB01101.1" />
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308 <has_text text="HMDB10348" />
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309 <has_text text="HMDB59717" />
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310 <not_has_text text="HMDB13189" />
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311 <has_text text="HMDB00299" />
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312 <has_text text="HMDB00191" />
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313 <has_text text="HMDB00518" />
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314 <has_text text="HMDB00715" />
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315 <has_text text="HMDB01032" />
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316 <has_text text="HMDB00208" />
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317 <has_text text="HMDB04824" />
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318 <has_text text="HMDB00512" />
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319 <has_text text="HMDB00251" />
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320 </assert_contents>
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321 </output>
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322 </test>
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323 <test>
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324 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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325 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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326 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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327 <param name="classnameColumn" value="gender"/>
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328 <param name="sampleclassNames" value="[Mm],[fF]"/>
5
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329 <param name="wildcards" value="FALSE"/>
4
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330 <param name="samplenameColumn" value="sampleMetadata"/>
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331 <param name="inclusive" value="filter-in"/>
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332 <output name="sampleMetadata_out">
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333 <assert_contents>
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334 <has_text text="HU_028" />
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335 <has_text text="HU_051" />
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336 <has_text text="HU_060" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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337 <has_text text="HU_110" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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338 <has_text text="HU_149" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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339 <has_text text="HU_152" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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340 <has_text text="HU_175" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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341 <has_text text="HU_178" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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342 <has_text text="HU_185" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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343 <not_has_text text="HU_204" />
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344 <has_text text="HU_208" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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345 <has_text text="HU_017" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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346 <has_text text="HU_034" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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347 <has_text text="HU_078" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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348 <has_text text="HU_091" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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349 <has_text text="HU_093" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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350 <has_text text="HU_099" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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351 <has_text text="HU_130" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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352 <has_text text="HU_134" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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353 <has_text text="HU_138" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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354 </assert_contents>
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355 </output>
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356 </test>
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357 <test>
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358 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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359 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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360 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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361 <param name="classnameColumn" value=""/>
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362 <param name="sampleclassNames" value="M"/>
5
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363 <param name="wildcards" value="FALSE"/>
4
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364 <param name="samplenameColumn" value="sampleMetadata"/>
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365 <param name="inclusive" value="filter-in"/>
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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366 <output name="sampleMetadata_out">
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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367 <assert_contents>
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368 <has_text text="HU_028" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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369 <has_text text="HU_051" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
370 <has_text text="HU_060" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
371 <has_text text="HU_110" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
372 <has_text text="HU_149" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
373 <has_text text="HU_152" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
374 <has_text text="HU_175" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
375 <has_text text="HU_178" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
376 <has_text text="HU_185" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
377 <not_has_text text="HU_204" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
378 <has_text text="HU_208" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
379 <has_text text="HU_017" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
380 <has_text text="HU_034" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
381 <has_text text="HU_078" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
382 <has_text text="HU_091" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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383 <has_text text="HU_093" />
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384 <has_text text="HU_099" />
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385 <has_text text="HU_130" />
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386 <has_text text="HU_134" />
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387 <has_text text="HU_138" />
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388 </assert_contents>
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389 </output>
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390 </test>
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391 </tests>
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392
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393
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394
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395 <help><![CDATA[
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396
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397
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398 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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399
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400 --------------------------------------------------------------------------
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401
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402
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403 **R package**
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404
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405 The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
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406
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407 -----------------------------------------------------------------------------------------------------------------------------------------
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408
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409
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410 **Tool updates**
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411
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412 See the **NEWS** section at the bottom of this page
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413
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414 ---------------------------------------------------
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415
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416 ==============================================
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417 Filter Workflow4Metabolomics data matrix files
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418 ==============================================
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419
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420 -----------
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421 Description
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422 -----------
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423
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424 Filter a set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample-class
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425
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426 -----------------
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427 Workflow Position
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428 -----------------
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429
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430 - Upstream tool category: Preprocessing
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431 - Downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
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432
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433 ----------
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434 Motivation
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435 ----------
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436
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437 GC-MS1 and LC-MS1 experiments seek to resolve chemicals as features that have distinct chromatographic behavior and (after ionization) mass-to-charge ratio.
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438 Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of m/z ratio and chromatographic retention time.
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439 Ideally, features would be sufficiently reproducible from sample-run to sample-run to identify features that are commmon among samples and those that differ.
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440 However, the chromatographic retention time for a chemical can vary from one run to another.
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441 In the Workflow4Metabolomics (W4M, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017]) "flavor" of Galaxy, the XCMS [Smith *et al.*, 2006] preprocessing tools provide for "retention time correction" to align features among samples, but features may be better aligned if pooled samples and blanks are included.
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442
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443 Multivariate statistical techniques may be used to discover clusters of similar samples, and sometimes it is desirable to apply clustering iteratively to smaller and smaller subsets of samples until observable separation of clusters is no longer significant.
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444 Once feature-alignment has been achieved among samples in GC-MS and LC-MS datasets, however, the presence of pools and blanks may confound identification and separation of clusters.
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445 Multivariate statistical algorithms also may be impacted by missing values or dimensions that have zero variance (Thévenot *et al.*, 2015).
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446
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447 The w4mclassfilter tool provides a way to choose subsets of samples for further analysis.
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448 The tool takes as input the data matrix, sample metadata, and variable metadata Galaxy datasets produced by W4M and produces the same trio of datasets with data only for the selected samples.
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449 The tool uses a "sample-class" column in the sample metadata as the basis for including or eliminating samples for further analysis.
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450 Class-values to be considered are provided by the user as a comma-separated list.
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451 The user also provides an indication whether the list specifies classes to be included in further analysis ("filter-in") or rather to be excluded from it ("filter-out").
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452 Next, missing and negative intensites for features of the remaining samples are imputed to zero.
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453 Finally, samples or features with zero variance are eliminated.
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454
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455 -----------
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456 Input files
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457 -----------
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458
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459 +---------------------------+------------+
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460 | File | Format |
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461 +===========================+============+
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462 | Data matrix | tabular |
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463 +---------------------------+------------+
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464 | Sample metadata | tabular |
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465 +---------------------------+------------+
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466 | Variable metadata | tabular |
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467 +---------------------------+------------+
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468
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469
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470 ----------
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471 Parameters
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472 ----------
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473
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474 Data matrix file
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475 | variable x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
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476 |
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477
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478 Sample metadata file
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479 | 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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480 |
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481
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482 Variable metadata file
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483 | 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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484 |
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485
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486 Column that names the sample (default = '``sampleMetadata``')
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487 | name of the column in sample metadata that has the name of the sample
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488 |
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489
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490 Column that names the sample-class (default = '``class``')
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491 | name of the column in sample metadata that has the values to be tested against the '``classes``' input parameter
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492 |
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493
0
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494 Names of sample classes (default = no names)
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495 | comma-separated names of sample classes to include or exclude
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496 |
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497
4
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498 Wild-cards (default = '``wild-cards``')
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499 | '``wild-cards``' - use wild-cards to match names of sample classes (see 'Wild card patterns to match class-names' below)
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500 | '``regular-expressions``' - exclude only the named sample classes (see 'Regular expression patterns to match class-names' below)
0
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501 |
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502
4
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503 Include named classes (default = '``filter-out``')
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504 | '``filter-in``' - include only the named sample classes
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505 | '``filter-out``' - exclude only the named sample classes
0
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506 |
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507
6
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508 Variable-range filters (default = no filters)
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509 | comma-separated names of variable-range filters (see 'Variable-range filters' below)
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510 |
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511
0
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512
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513
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514 ------------
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515 Output files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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516 ------------
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517
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518
2
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519 sampleMetadata
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520 | (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples (xC-MS features) that have been filtered out (by the sample-class filter or because of zero variance)
0
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521 |
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522
2
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523 variableMetadata
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524 | (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 (because of zero variance)
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525 |
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526
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527 dataMatrix
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528 | (tabular separated values) file identical to the **dataMatrix** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) and columns that have been filtered out (by the sample-class filter or because of zero variance)
0
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529 |
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530
2
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531
4
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532 ---------------------------------------
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533 Wild card patterns to match class-names
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534 ---------------------------------------
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535
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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536 Beginning with v0.98.2, w4mclassfilter supports use of R "wild card" patterns to select class-names.
4
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537
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538 - use '``?``' to match a single character
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539 - use '``*``' to match zero or more characters
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540 - the entire pattern must match the sample name
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541
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542 For example
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543
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544 - '``??.samp*``' matches '``my.sample``' but not '``my.own.sample``'
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545 - '``*.sample``' matches '``my.sample``' and '``my.own.sample``'
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546 - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``'
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547
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548 ------------------------------------------------
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549 Regular expression patterns to match class-names
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550 ------------------------------------------------
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551
5
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552 Beginning with v0.98.2, w4mclassfilter supports use of R "regular expression" patterns to select class-names.
4
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553
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554 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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555 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
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556
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557 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
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558
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559 - '``^``' matches the beginning of a class-name
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560 - '``$``' matches the end of a class-name
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561 - '``.``' outside of square brackets matches a single character
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562 - '``*``' matches character specified immediately before zero or more times
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563 - square brackets specify a set of characters to be matched.
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564
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565 Within square brackets
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566
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567 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
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568 - '``-``' is used to specify ranges of characters
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569
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570 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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571
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572 First Example: Consider a field of class-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
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573
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574 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
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575 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
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576 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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577 - The regular expression '``^[a-z][a-z][0-9]$``' 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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578
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579 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
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diff changeset
580
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581 - '``^[A-Z][A-Z][0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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582 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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583 - '``^[A-Z][0-9]*``' - MATCHES '``**^A** B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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584 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
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585 - '``^[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.
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586 - '``^[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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587
6
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588 ----------------------
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589 Variable-range filters
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590 ----------------------
4
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591
6
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592 An array of range-specification strings may be supplied in the `variableRangeFilter`
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593 argument. If supplied, only features having numerical values in the specified column
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594 of `variableMetadata` that fall within the specified ranges will be retained
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595 in the output. Each range is a string of three colon-separated values (e.g., "mz:200:800") in the
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596 following order:
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597
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598 - the **name of a column of `variableMetadata`** which must have numerical data (e.g., "mz");
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599 - the **minimum allowed value** in that column for the feature to be retained (e.g., 200);
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600 - the **maximum allowed value** (e.g., 800).
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601
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602 Note for the range specification strings:
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603
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604 - **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)
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605 - **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.
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606
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607 - 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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608
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609 -----------------------------------------------------------------------------
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610
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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611 ----------------
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612 WORKING EXAMPLES
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613 ----------------
2
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614
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615 .. class:: infomark
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616
6
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617 -----------
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618 Input Files
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619 -----------
2
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620
6
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621 +------------------------------------------------------------------------------------------------------------------------+
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622 | Input File URL |
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623 +========================================================================================================================+
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624 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_dataMatrix.tsv |
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625 +------------------------------------------------------------------------------------------------------------------------+
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626 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_sampleMetadata.tsv |
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627 +------------------------------------------------------------------------------------------------------------------------+
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628 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/input_variableMetadata.tsv |
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629 +------------------------------------------------------------------------------------------------------------------------+
2
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630
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631 .. class:: infomark
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632
6
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633 -------------------------------
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634 Running Without Range-Filtering
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635 -------------------------------
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636
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637 This example retains only samples whose 'gender' attribute is 'M'.
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638
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639 **Input parameters**
0
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640
2
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641 +------------------------------------+-----------------+
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642 | Input Parameter | Value |
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643 +====================================+=================+
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644 | Names of sample classes | M |
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645 +------------------------------------+-----------------+
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646 | Include named classes | filter-in |
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647 +------------------------------------+-----------------+
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648 | Column that names the sample-class | gender |
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649 +------------------------------------+-----------------+
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650 | Column that names the sample | sampleMetadata |
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651 +------------------------------------+-----------------+
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652
6
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653 **Expected outputs**
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654
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655 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
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656 | Expected Output | Download from URL |
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657 +===================+===========================================================================================================================+
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658 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_dataMatrix.tsv |
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659 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
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660 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_sampleMetadata.tsv |
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661 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
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662 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/expected_variableMetadata.tsv |
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663 +-------------------+---------------------------------------------------------------------------------------------------------------------------+
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664
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665 .. class:: infomark
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666
6
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667 ----------------------------
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668 Running With Range-Filtering
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669 ----------------------------
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670
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671 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.
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672 This example retains all samples (except those having zero variance for all feature), although it would be possible to filter on samples as well.
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673
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674 **Input parameters**
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675
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676 +------------------------------------+-------------------------------+
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677 | Input Parameter | Value |
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678 +====================================+===============================+
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679 | Names of sample classes | (Leave this field empty.) |
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680 +------------------------------------+-------------------------------+
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681 | Include named classes | filter-out |
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682 +------------------------------------+-------------------------------+
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683 | Column that names the sample-class | class |
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684 +------------------------------------+-------------------------------+
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685 | Column that names the sample | sampleMetadata |
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686 +------------------------------------+-------------------------------+
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687 | Variable range-filters | FEATMAX:2e6:,mz:200:,rt::800 |
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
688 +------------------------------------+-------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
689
2
23c6d271def9 planemo upload
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diff changeset
690 **Expected outputs**
23c6d271def9 planemo upload
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diff changeset
691
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
692 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
693 | Expected Output | Download from URL |
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
694 +===================+==============================================================================================================================+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
695 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_dataMatrix.tsv |
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
696 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
697 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_sampleMetadata.tsv |
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
698 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
699 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/test-data/rangefilter_variableMetadata.tsv |
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
700 +-------------------+------------------------------------------------------------------------------------------------------------------------------+
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
701
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
702 -----------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
703
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
704 ----
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
705 NEWS
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
706 ----
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
707
7
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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diff changeset
708 CHANGES IN VERSION 0.98.7
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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diff changeset
709 =========================
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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parents: 6
diff changeset
710
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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parents: 6
diff changeset
711 New features
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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parents: 6
diff changeset
712
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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parents: 6
diff changeset
713 * First column of output variableMetadata (that has feature names) now is always named "variableMetadata".
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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parents: 6
diff changeset
714 * First column of output sampleMetadata now (that has sample names) is always named "sampleMetadata".
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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parents: 6
diff changeset
715
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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parents: 6
diff changeset
716 Internal modifications
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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parents: 6
diff changeset
717
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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parents: 6
diff changeset
718 * Now uses w4mclassfilter R package v0.98.7.
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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parents: 6
diff changeset
719
582a8a42a93b planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b8d012c6d259a0ce736e2cff501990b35dabd704
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diff changeset
720 CHANGES IN VERSION 0.98.6
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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parents: 4
diff changeset
721 =========================
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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parents: 4
diff changeset
722
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
723 New features
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
724
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
725 * Added support for filtering out features whose attributes fall outside specified ranges.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
726 For more detail, see "Variable-range filters" above.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
727
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
728 Internal modifications
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
729
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
730 * Now uses w4mclassfilter R package v0.98.6.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
731 * Now sorts sample names and feature names in output files because some statistical tools expect the same order in `dataMatrix` row and column names as in the corresponding metadata 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
732
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
733 Changes in version 0.98.3
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
734 =========================
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
735
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
736 Internal modifications
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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parents: 4
diff changeset
737
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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parents: 4
diff changeset
738 * Improved input handling.
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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parents: 4
diff changeset
739 * Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool.
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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parents: 4
diff changeset
740 * Improved reference-list.
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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parents: 4
diff changeset
741
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
742 Changes in version 0.98.2
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
743 =========================
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
744
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
745 New features
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
746
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
747 * Added support for R-flavored regular expression pattern-matching when selecting names of sample-classes.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
748 * Empty classes argument or zero-length class_column result in no samples filtered out.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
749
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
750 Internal modifications
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
751
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
752 * Support and tests for new features.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
753
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
754 Changes in version 0.98.1
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
755 =========================
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
756
3
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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diff changeset
757 First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
758
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
759 New features
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
760
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
761 * *dataMatrix* *is* modified by the tool, so it *does* appear as an output file
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
762 * *sampleMetadata* *is* modified by the tool, so it *does* appear as an output file
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
763 * *variableMetadata* *is* modified by the tool, so it *does* appear as an output file
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
764
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
765 Internal modifications
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
766
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
767 * N/A
3
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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parents: 2
diff changeset
768
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
769 ]]></help>
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
770 <citations>
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
771 <!-- Giacomoni_2014 W4M 2.5 -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
772 <citation type="doi">10.1093/bioinformatics/btu813</citation>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
773 <!-- Guitton_2017 W4M 3.0 -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
774 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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parents: 4
diff changeset
775 <!-- Smith_2006 XCMS -->
3
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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diff changeset
776 <citation type="doi">10.1021/ac051437y</citation>
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
777 <!-- Th_venot_2015 Urinary metabolome statistics -->
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
778 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
779 </citations>
3
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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diff changeset
780 <!--
7
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781 vim:noet:sw=2:ts=2
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191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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782 --> </tool>