Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 11:9f5c0e23c205 draft

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planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 32cf96ed6c39a93eb9c6cf00494b128bd3c3febe
author eschen42
date Mon, 03 Sep 2018 22:34:35 -0400
parents 649cb1bafd3e
children 38f509903a0b
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11
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1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.11">
10
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2 <description>Filter W4m data by values or metadata</description>
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3 <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation: http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/ -->
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4 <requirements>
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5 <!-- <requirement type="package" version="6.2">readline</requirement> -->
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6 <requirement type="package" version="3.4.1">r-base</requirement>
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7 <requirement type="package" version="1.1_4">r-batch</requirement>
11
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8 <requirement type="package" version="0.98.8">w4mclassfilter</requirement>
10
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9 </requirements>
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10 <command detect_errors="aggressive"><![CDATA[
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11 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
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12 dataMatrix_in '$dataMatrix_in'
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13 sampleMetadata_in '$sampleMetadata_in'
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14 variableMetadata_in '$variableMetadata_in'
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15 sampleclassNames '$sampleclassNames'
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16 inclusive '$inclusive'
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17 wildcards '$wildcards'
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18 classnameColumn '$classnameColumn'
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19 samplenameColumn 'sampleMetadata'
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20 variable_range_filter '$variableRangeFilter'
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21 transformation '$transformation'
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22 dataMatrix_out '$dataMatrix_out'
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23 sampleMetadata_out '$sampleMetadata_out'
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24 variableMetadata_out '$variableMetadata_out'
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25 ]]></command>
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26 <inputs>
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27 <param name="dataMatrix_in" format="tabular" label="Data matrix file" type="data"
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28 help="variables &#10006; samples" />
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29 <param name="sampleMetadata_in" format="tabular" label="Sample metadata file" type="data"
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30 help="sample metadata, one row per sample" />
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31 <param name="variableMetadata_in" format="tabular" label="Variable metadata file" type="data"
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32 help="variable metadata, one row per variable" />
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33 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class"
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34 help="name of the column in sample metadata that has the values to be tested against the 'Names of sample-classes' input parameter - defaults to 'class'">
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35 <sanitizer>
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36 <valid initial="string.letters">
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37 <add preset="string.digits"/>
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38 <add value="&#46;" /> <!-- dot, period -->
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39 <add value="&#95;" /> <!-- underscore -->
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40 </valid>
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41 </sanitizer>
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42 </param>
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43 <param name="sampleclassNames" label="Names of sample-classes" type="text" value = ""
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44 help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names">
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45 <sanitizer>
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46 <valid initial="string.letters">
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47 <add preset="string.digits"/>
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48 <add value="&#123;" /> <!-- l-cube, left-curly-bracket -->
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49 <add value="&#124;" /> <!-- pipe -->
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50 <add value="&#125;" /> <!-- r-cube, right-curly-bracket -->
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51 <add value="&#36;" /> <!-- dollar, dollar-sign -->
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52 <add value="&#40;" /> <!-- left-paren -->
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53 <add value="&#41;" /> <!-- right-paren -->
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54 <add value="&#42;" /> <!-- splat, asterisk -->
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55 <add value="&#43;" /> <!-- plus -->
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56 <add value="&#45;" /> <!-- dash, hyphen -->
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57 <add value="&#44;" /> <!-- comma -->
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58 <add value="&#46;" /> <!-- dot, period -->
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59 <add value="&#58;" /> <!-- colon -->
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60 <add value="&#59;" /> <!-- semi, semicolon -->
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61 <add value="&#63;" /> <!-- what, question mark -->
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62 <add value="&#91;" /> <!-- l-squib, left-squre-bracket -->
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63 <add value="&#92;" /> <!-- whack, backslash -->
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64 <add value="&#93;" /> <!-- r-squib, right-squre-bracket -->
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65 <add value="&#94;" /> <!-- hat, caret -->
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66 <add value="&#95;" /> <!-- underscore -->
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67 </valid>
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68 </sanitizer>
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69 </param>
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70 <param name="wildcards" label="Use 'wild cards' or 'regular expressions'" type="select"
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71 help="'wild-cards' (the default) - use '*' and '?' to match class names; 'regular-expressions' - use regular expressions to match class names">
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72 <option value="TRUE" selected="true">wild-cards</option>
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73 <option value="FALSE">regular-expressions</option>
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74 </param>
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75 <param name="inclusive" label="Exclude/include named classes" type="select"
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76 help="'filter-out' (the default) - exclude only the named sample-classes; 'filter-in' - include only the named sample-classes">
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77 <option value="TRUE">filter-in</option>
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78 <option value="FALSE" selected="true">filter-out</option>
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79 </param>
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80 <param name="variableRangeFilter" label="Variable-range filters" type="text" value = ""
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81 help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)">
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82 <sanitizer>
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83 <valid initial="string.letters">
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84 <add preset="string.digits"/>
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85 <add value="&#44;" /> <!-- comma -->
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86 <add value="&#46;" /> <!-- dot, period -->
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87 <add value="&#58;" /> <!-- colon -->
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88 <add value="&#95;" /> <!-- underscore -->
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89 </valid>
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90 </sanitizer>
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91 </param>
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92 <param name="transformation" label="Data-transformation" type="select"
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93 help="'none' (the default) - do not transform data; 'log2' - log base 2 of data; 'log10' - log base 10 of data; in all cases, negative and missing values are imputed to zero">
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94 <option value="none" selected="true">none</option>
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95 <option value="log2">log2</option>
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96 <option value="log10">log10</option>
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97 </param>
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98 </inputs>
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99 <outputs>
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100 <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>
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101 <data name="sampleMetadata_out" format="tabular" label="${sampleMetadata_in.name}.subset" ></data>
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102 <data name="variableMetadata_out" format="tabular" label="${variableMetadata_in.name}.subset" ></data>
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103 </outputs>
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104 <tests>
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105 <!-- test 1 -->
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106 <test>
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107 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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108 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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109 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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110 <param name="classnameColumn" value="gender"/>
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111 <param name="sampleclassNames" value="M"/>
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112 <param name="wildcards" value="FALSE"/>
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113 <param name="inclusive" value="filter-in"/>
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114 <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
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115 <param name="transformation" value="log10"/>
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116 <output name="dataMatrix_out">
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117 <assert_contents>
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118 <has_text text="5.87336711011293" />
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119 </assert_contents>
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120 </output>
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121 <output name="sampleMetadata_out">
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122 <assert_contents>
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123 <not_has_text text="HU_028" />
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124 <not_has_text text="HU_051" />
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125 <not_has_text text="HU_060" />
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126 <not_has_text text="HU_110" />
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127 <not_has_text text="HU_149" />
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128 <not_has_text text="HU_152" />
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129 <not_has_text text="HU_175" />
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130 <not_has_text text="HU_178" />
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131 <not_has_text text="HU_185" />
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132 <not_has_text text="HU_204" />
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133 <not_has_text text="HU_208" />
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134 <has_text text="HU_017" />
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135 <has_text text="HU_034" />
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136 <has_text text="HU_078" />
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137 <has_text text="HU_091" />
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138 <has_text text="HU_093" />
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139 <has_text text="HU_099" />
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140 <has_text text="HU_130" />
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141 <has_text text="HU_134" />
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142 <has_text text="HU_138" />
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143 </assert_contents>
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144 </output>
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145 <output name="variableMetadata_out">
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146 <assert_contents>
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147 <not_has_text text="HMDB00191" />
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148 <has_text text="HMDB00208" />
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149 <not_has_text text="HMDB00251" />
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150 <not_has_text text="HMDB00299" />
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151 <not_has_text text="HMDB00512" />
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152 <not_has_text text="HMDB00518" />
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153 <not_has_text text="HMDB00715" />
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154 <not_has_text text="HMDB00822" />
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155 <has_text text="HMDB01032" />
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156 <has_text text="HMDB01101.1" />
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157 <not_has_text text="HMDB03193" />
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158 <not_has_text text="HMDB04824" />
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159 <not_has_text text="HMDB10348" />
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160 <has_text text="HMDB13189" />
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161 <not_has_text text="HMDB59717" />
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162 </assert_contents>
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163 </output>
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164 </test>
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165 <!-- test 2 -->
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166 <test>
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167 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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168 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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169 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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170 <param name="classnameColumn" value="sampleMetadata"/>
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171 <!-- test that hyphens in regular expressions work -->
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172 <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/>
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173 <param name="wildcards" value="FALSE"/>
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174 <param name="inclusive" value="filter-in"/>
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175 <param name="variableRangeFilter" value="FEATMAX:20.93157:,mz:200:,rt::800"/>
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176 <param name="transformation" value="log2"/>
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177 <output name="dataMatrix_out">
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178 <assert_contents>
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179 <has_text text="19.5109032146715" />
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180 </assert_contents>
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181 </output>
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182 <output name="sampleMetadata_out">
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183 <assert_contents>
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184 <has_text text="HU_028" />
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185 <has_text text="HU_051" />
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186 <has_text text="HU_060" />
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187 <has_text text="HU_110" />
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188 <has_text text="HU_149" />
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189 <has_text text="HU_152" />
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190 <has_text text="HU_175" />
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191 <has_text text="HU_178" />
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192 <has_text text="HU_185" />
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193 <not_has_text text="HU_204" />
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194 <has_text text="HU_208" />
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195 <has_text text="HU_017" />
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196 <has_text text="HU_034" />
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197 <has_text text="HU_078" />
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198 <has_text text="HU_091" />
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199 <has_text text="HU_093" />
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200 <has_text text="HU_099" />
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201 <has_text text="HU_130" />
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202 <has_text text="HU_134" />
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203 <has_text text="HU_138" />
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204 </assert_contents>
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205 </output>
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206 <output name="variableMetadata_out">
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207 <assert_contents>
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208 <has_text text="HMDB00191" />
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209 <has_text text="HMDB00208" />
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210 <not_has_text text="HMDB00251" />
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211 <not_has_text text="HMDB00299" />
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212 <not_has_text text="HMDB00512" />
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213 <not_has_text text="HMDB00518" />
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214 <not_has_text text="HMDB00715" />
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215 <not_has_text text="HMDB00822" />
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216 <has_text text="HMDB01032" />
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217 <has_text text="HMDB01101.1" />
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218 <not_has_text text="HMDB03193" />
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219 <not_has_text text="HMDB04824" />
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220 <not_has_text text="HMDB10348" />
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221 <has_text text="HMDB13189" />
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222 <not_has_text text="HMDB59717" />
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223 </assert_contents>
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224 </output>
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225 </test>
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226 <!-- test 3 -->
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227 <test>
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228 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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229 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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230 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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231 <param name="classnameColumn" value="gender"/>
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232 <param name="sampleclassNames" value="M"/>
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233 <param name="inclusive" value="filter-in"/>
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234 <param name="transformation" value="none"/>
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235 <output name="dataMatrix_out">
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236 <assert_contents>
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237 <not_has_text text="HU_028" />
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238 <not_has_text text="HU_051" />
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239 <not_has_text text="HU_060" />
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240 <not_has_text text="HU_110" />
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241 <not_has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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242 <not_has_text text="HU_152" />
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243 <not_has_text text="HU_175" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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244 <not_has_text text="HU_178" />
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245 <not_has_text text="HU_185" />
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246 <not_has_text text="HU_204" />
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247 <not_has_text text="HU_208" />
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248 <has_text text="HU_017" />
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249 <has_text text="HU_034" />
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250 <has_text text="HU_078" />
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251 <has_text text="HU_091" />
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252 <has_text text="HU_093" />
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253 <has_text text="HU_099" />
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254 <has_text text="HU_130" />
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255 <has_text text="HU_134" />
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256 <has_text text="HU_138" />
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257 <has_text text="HMDB03193" />
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258 <not_has_text text="HMDB00822" />
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259 <has_text text="HMDB01101" />
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260 <has_text text="HMDB01101.1" />
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261 <has_text text="HMDB10348" />
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262 <has_text text="HMDB59717" />
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263 <has_text text="HMDB13189" />
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264 <has_text text="HMDB00299" />
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265 <has_text text="HMDB00191" />
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266 <has_text text="HMDB00518" />
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267 <has_text text="HMDB00715" />
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268 <has_text text="HMDB01032" />
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269 <has_text text="HMDB00208" />
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270 <has_text text="HMDB04824" />
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271 <has_text text="HMDB00512" />
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272 <has_text text="HMDB00251" />
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273 </assert_contents>
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274 </output>
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275 </test>
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276 <!-- test 4 -->
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277 <test>
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278 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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279 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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280 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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281 <param name="classnameColumn" value="gender"/>
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282 <param name="sampleclassNames" value="*"/>
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283 <param name="wildcards" value="TRUE"/>
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284 <param name="inclusive" value="filter-in"/>
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285 <output name="sampleMetadata_out">
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286 <assert_contents>
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287 <not_has_text text="HU_204" />
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288 <has_text text="HU_028" />
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289 <has_text text="HU_051" />
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290 <has_text text="HU_060" />
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291 <has_text text="HU_110" />
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292 <has_text text="HU_149" />
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293 <has_text text="HU_152" />
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294 <has_text text="HU_175" />
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295 <has_text text="HU_178" />
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296 <has_text text="HU_185" />
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297 <has_text text="HU_208" />
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298 <has_text text="HU_017" />
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299 <has_text text="HU_034" />
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300 <has_text text="HU_078" />
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301 <has_text text="HU_091" />
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302 <has_text text="HU_093" />
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303 <has_text text="HU_099" />
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304 <has_text text="HU_130" />
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305 <has_text text="HU_134" />
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306 <has_text text="HU_138" />
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307 </assert_contents>
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308 </output>
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309 </test>
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310 <!-- test 5 -->
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311 <test>
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312 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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313 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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314 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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315 <param name="classnameColumn" value="gender"/>
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316 <param name="sampleclassNames" value="M"/>
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317 <param name="wildcards" value="FALSE"/>
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318 <param name="inclusive" value="filter-in"/>
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319 <output name="sampleMetadata_out">
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320 <assert_contents>
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321 <not_has_text text="HU_028" />
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322 <not_has_text text="HU_051" />
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323 <not_has_text text="HU_060" />
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324 <not_has_text text="HU_110" />
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325 <not_has_text text="HU_149" />
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326 <not_has_text text="HU_152" />
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327 <not_has_text text="HU_175" />
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328 <not_has_text text="HU_178" />
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329 <not_has_text text="HU_185" />
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330 <not_has_text text="HU_204" />
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331 <not_has_text text="HU_208" />
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332 <has_text text="HU_017" />
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333 <has_text text="HU_034" />
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334 <has_text text="HU_078" />
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335 <has_text text="HU_091" />
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336 <has_text text="HU_093" />
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337 <has_text text="HU_099" />
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338 <has_text text="HU_130" />
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339 <has_text text="HU_134" />
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340 <has_text text="HU_138" />
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341 </assert_contents>
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342 </output>
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343 </test>
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344 <!-- test 6 -->
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345 <test>
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346 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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347 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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348 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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349 <param name="classnameColumn" value="gender"/>
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350 <param name="sampleclassNames" value="M"/>
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351 <param name="wildcards" value="FALSE"/>
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352 <param name="inclusive" value="filter-in"/>
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353 <output name="variableMetadata_out">
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354 <assert_contents>
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355 <has_text text="HMDB03193" />
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356 <not_has_text text="HMDB00822" />
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357 <has_text text="HMDB01101" />
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358 <has_text text="HMDB01101.1" />
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359 <has_text text="HMDB10348" />
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360 <has_text text="HMDB59717" />
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361 <has_text text="HMDB13189" />
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362 <has_text text="HMDB00299" />
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363 <has_text text="HMDB00191" />
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364 <has_text text="HMDB00518" />
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365 <has_text text="HMDB00715" />
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366 <has_text text="HMDB01032" />
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367 <has_text text="HMDB00208" />
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368 <has_text text="HMDB04824" />
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369 <has_text text="HMDB00512" />
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370 <has_text text="HMDB00251" />
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371 </assert_contents>
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372 </output>
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373 </test>
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374 <!-- test 7 -->
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375 <test>
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376 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/>
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377 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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378 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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379 <param name="classnameColumn" value="gender"/>
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380 <param name="sampleclassNames" value="M"/>
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381 <param name="wildcards" value="FALSE"/>
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382 <param name="inclusive" value="filter-in"/>
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383 <output name="variableMetadata_out">
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384 <assert_contents>
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385 <has_text text="HMDB03193" />
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diff changeset
386 <not_has_text text="HMDB00822" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
387 <has_text text="HMDB01101" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
388 <has_text text="HMDB01101.1" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
389 <has_text text="HMDB10348" />
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diff changeset
390 <has_text text="HMDB59717" />
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diff changeset
391 <not_has_text text="HMDB13189" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
392 <has_text text="HMDB00299" />
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diff changeset
393 <has_text text="HMDB00191" />
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diff changeset
394 <has_text text="HMDB00518" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
395 <has_text text="HMDB00715" />
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diff changeset
396 <has_text text="HMDB01032" />
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diff changeset
397 <has_text text="HMDB00208" />
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diff changeset
398 <has_text text="HMDB04824" />
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diff changeset
399 <has_text text="HMDB00512" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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400 <has_text text="HMDB00251" />
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401 </assert_contents>
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402 </output>
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403 </test>
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404 <!-- test 8 -->
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405 <test>
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406 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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407 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
408 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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409 <param name="classnameColumn" value="gender"/>
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410 <param name="sampleclassNames" value="[Mm],[fF]"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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411 <param name="wildcards" value="FALSE"/>
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412 <param name="inclusive" value="filter-in"/>
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413 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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414 <assert_contents>
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diff changeset
415 <has_text text="HU_028" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
416 <has_text text="HU_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
417 <has_text text="HU_060" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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418 <has_text text="HU_110" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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419 <has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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420 <has_text text="HU_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
421 <has_text text="HU_175" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
422 <has_text text="HU_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
423 <has_text text="HU_185" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
424 <not_has_text text="HU_204" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
425 <has_text text="HU_208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
426 <has_text text="HU_017" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
427 <has_text text="HU_034" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
428 <has_text text="HU_078" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
429 <has_text text="HU_091" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
430 <has_text text="HU_093" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
431 <has_text text="HU_099" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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432 <has_text text="HU_130" />
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433 <has_text text="HU_134" />
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434 <has_text text="HU_138" />
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435 </assert_contents>
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436 </output>
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437 </test>
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438 <!-- test 9 -->
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439 <test>
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440 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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441 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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442 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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443 <param name="classnameColumn" value=""/>
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444 <param name="sampleclassNames" value="M"/>
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445 <param name="wildcards" value="FALSE"/>
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446 <param name="inclusive" value="filter-in"/>
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447 <output name="sampleMetadata_out">
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448 <assert_contents>
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449 <has_text text="HU_028" />
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450 <has_text text="HU_051" />
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451 <has_text text="HU_060" />
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452 <has_text text="HU_110" />
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453 <has_text text="HU_149" />
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454 <has_text text="HU_152" />
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455 <has_text text="HU_175" />
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456 <has_text text="HU_178" />
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457 <has_text text="HU_185" />
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458 <not_has_text text="HU_204" />
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459 <has_text text="HU_208" />
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460 <has_text text="HU_017" />
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461 <has_text text="HU_034" />
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462 <has_text text="HU_078" />
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463 <has_text text="HU_091" />
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464 <has_text text="HU_093" />
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465 <has_text text="HU_099" />
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466 <has_text text="HU_130" />
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467 <has_text text="HU_134" />
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468 <has_text text="HU_138" />
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469 </assert_contents>
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470 </output>
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471 </test>
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472 </tests>
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473 <help><![CDATA[
0
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474
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475
5
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476 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
0
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477
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478 --------------------------------------------------------------------------
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479
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480
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481 **R package**
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482
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483 The *w4mclassfilter* package (which is used by the W4m Data Subset tool) is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
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484
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485 -----------------------------------------------------------------------------------------------------------------------------------------
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486
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487
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488 **Tool updates**
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489
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490 See the **NEWS** section at the bottom of this page
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491
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492 ---------------------------------------------------
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493
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494 ===========================================================
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495 "W4m Data Subset" - Filter Workflow4Metabolomics data files
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496 ===========================================================
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497
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498 ----------
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499 Motivation
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500 ----------
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501
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502 GC-MS and LC-MS experiments seek to resolve as features chemicals that have distinct chromatographic retention-time ("rt") and (after ionization) mass-to-charge ratio ("m/z" or "mz").
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503 (If the MS protocol includes fragmentation, several features may result for each chemical.)
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504 Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of rt and m/z.
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505 Ideally, features would be sufficiently reproducible among sample-runs to distinguish features that are commmon among samples from those that differ.
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506
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507 The chromatographic retention-time for a chemical can vary from one chromatography run to the next.
8
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508 Workflow4Metabolomics (W4m, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017]) is a "flavor" of Galaxy that uses the XCMS preprocessing tools for "retention-time correction" to align features among samples.
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509 Features may be better aligned if pooled samples and blanks are included.
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510
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511 Multivariate statistical techniques may be used to discover clusters of similar samples (Th]]>&#233;<![CDATA[venot *et al.*, 2015).
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512 However, once retention-time alignment of features has been achieved among samples in GC-MS and LC-MS datasets:
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513
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514 - The presence of pools and blanks may confound identification and separation of clusters.
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515 - Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance.
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516
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517 -----------
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518 Description
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519 -----------
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520
8
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521 The **W4m Data Subset** tool **selects subsets of samples, features, or data values** for further analysis.
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522
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523 - The tool takes as input the data matrix, sample metadata, and variable metadata datasets produced by W4m's XCMS [Smith *et al.*, 2006] and CAMERA [Kuhl *et al.*, 2012] tools.
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524 - The tool produces the same trio of output datasets, modified as follows.
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525
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526 This tool can perform several operations to reduce the number samples or features to be analyzed (although **this should be done only in a statistically sound manner** consistent with the nature of the experiment):
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527
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528 - Samples may be eliminated by filtering on a designated “sample class” column in sampleMetadata.
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529 - Features may be eliminated by specifying minimum or maximum value (or both) allowable in columns of variableMetadata.
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530 - Features may be eliminated by “range of row-maximum for each feature”, i.e., by specifying minimum or maximum intensity (or both) allowable in each row of the dataMatrix (i.e., for the feature across all samples).
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531
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532 This tool also performs several operations to address several data issues that may impede downstream statistical analysis:
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533
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534 - Missing values in dataMatrix are imputed to zero.
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535 - The values in the dataMatrix may be log-transformed if desired.
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536 - Samples that are missing from either sampleMetadata or dataMatrix are eliminated.
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537 - Features that are missing from either variableMetadata or dataMatrix are eliminated.
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538 - Features and samples that have zero variance are eliminated.
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539 - Samples and features are sorted alphabetically in rows and columns of dataMatrix and in rows of variableMetadata and sampleMetadata.
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540 - The names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata".
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541
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542 This tool may be applied several times sequentially, which may be useful for:
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543
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544 - analyzing subsets of samples for progressively smaller sets of treatment-levels, or
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545 - choosing subsets of samples based on criteria in several columns of the sampleMetadata table.
3
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546
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547 -----------------
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548 Workflow Position
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549 -----------------
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550
8
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551 This tool can be used at any point downstream of Preprocessing.
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552
8
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553 - Possible upstream tool categories: Preprocessing, Quality Control, Statistical Analysis, Filter and Sort
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554 - Possible downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
3
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555
0
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556 -----------
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557 Input files
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558 -----------
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559
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560 +---------------------------+------------+
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561 | File | Format |
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562 +===========================+============+
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563 | Data matrix | tabular |
0
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564 +---------------------------+------------+
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565 | Sample metadata | tabular |
0
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566 +---------------------------+------------+
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567 | Variable metadata | tabular |
0
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568 +---------------------------+------------+
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569
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570
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571 ----------
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572 Parameters
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573 ----------
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574
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575 Data matrix file
8
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576 | variable x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical, respectively, to the rownames of the sample metadata file and variable metadata file
0
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577 |
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578
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579 Sample metadata file
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580 | sample x metadata **sampleMetadata** (tabular separated values) file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
0
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581 |
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582
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583 Variable metadata file
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584 | variable x metadata **variableMetadata** (tabular separated values) file of the numeric and/or character variable metadata, with . as decimal and NA for missing values
0
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585 |
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586
8
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587 Column that names the sample-class (default = '``class``')
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588 | name of the column in **sampleMetadata** that has the values to be tested against the '``Names of sample-classes``' input parameter; only letters, digits, periods, and underscores are permitted.
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589 |
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590
8
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591 Names of sample-classes (default = no names)
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592 | comma-separated names (or regular expressions to match names) of sample-classes to include or exclude
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593 |
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594
8
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595 'Wild cards' or 'regular expressions' (default = '``wild-cards``')
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596 | '``wild-cards``' - use wild cards to match names of sample-classes (see the 'Wild card patterns to match class-names' section below)
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597 | '``regular-expressions``' - use regular expressions to match the named sample-classes (see the 'Regular expression patterns to match class-names' section below)
0
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598 |
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599
8
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600 Exclude/include named classes (default = '``filter-out``')
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601 | '``filter-in``' - include only the named sample-classes
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602 | '``filter-out``' - exclude only the named sample-classes
0
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603 |
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604
6
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605 Variable-range filters (default = no filters)
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606 | comma-separated names of variable-range filters (see the 'Variable-range filters' section below)
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607 |
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608
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609 Data-transformation (default = '``none``')
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610 | '``none``' - do not transform data matrix values
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611 | '``log2``' - take the log base 2 of the values in the data matrix
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612 | '``log10``' - take the log base 10 of the values in the data matrix
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613 | In both cases, negative and missing values are imputed to zero.
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614 |
0
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615
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616
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617 ------------
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618 Output files
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619 ------------
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620
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621 sampleMetadata
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622 | (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples that have been filtered out (by the sample-class filter, or because of zero variance, or because they were missing in the input data matrix)
0
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623 |
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624
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625 variableMetadata
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626 | (tabular separated values) file identical to the **variableMetadata** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (by the variable-range filter, or because of zero variance, or because they were missing in the input data matrix)
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627 |
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628
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629 dataMatrix
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630 | (tabular separated values) file identical to the **dataMatrix** file given as an input argument, excepting lacking rows and columns for variables and samples that have been filtered out, respectively
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631 |
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632
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633
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634 -----------------------------------------
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635 'Wild card' patterns to match class-names
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636 -----------------------------------------
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637
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638 W4m Data Subset supports use of R "wild card" patterns to select class-names.
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639
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640 - use '``?``' to match a single character
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641 - use '``*``' to match zero or more characters
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642 - the entire pattern must match the sample name
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643
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644 For example
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645
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646 - '``??.samp*``' matches '``my.sample``' but not '``my.own.sample``'
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647 - '``*.sample``' matches '``my.sample``' and '``my.own.sample``'
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648 - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``'
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649
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650 --------------------------------------------------
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651 'Regular expression' patterns to match class-names
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652 --------------------------------------------------
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653
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654 W4m Data Subset supports use of R "regular expression" patterns to select class-names.
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655
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656 R uses POSIX 1003.2 standard regular expressions, which allow precise pattern-matching and are exhaustively defined at:
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657 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
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658
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659 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
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660
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661 - '``^``' matches the beginning of a class-name
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662 - '``$``' matches the end of a class-name
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663 - '``.``' outside of square brackets matches a single character
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664 - '``*``' matches character specified immediately before zero or more times
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665 - square brackets specify a set of characters to be matched.
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666
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667 Within square brackets
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668
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669 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
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670 - '``-``' is used to specify ranges of characters
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671
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672 Caveat: The tool wrapper uses the comma ('``,``') to split a list of sample-class names, so **commas may not be used within regular expressions for this tool**
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673
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674 First Example: Consider a field of class-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
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675
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676 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
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677 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
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678 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
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679 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-classes as '``front3,front6,front9,marq3,marq6,marq9``'
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680
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681 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
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682
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683 - '``^[A-Z][A-Z][0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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684 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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685 - '``^[A-Z][0-9]*``' - MATCHES '``**^A** B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
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686 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
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687 - '``^[A-Z][A-Z]*[0-9][0-9]$``' - NO MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
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688 - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
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689
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690 ----------------------
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691 Variable-range filters
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692 ----------------------
4
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693
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694 An array of range-specification strings may be supplied in the `variableRangeFilter`
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695 argument. If supplied, only features having numerical values in the specified column
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696 of `variableMetadata` that fall within the specified ranges will be retained
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697 in the output. Each range is a string of three colon-separated values (e.g., "mz:200:800") in the
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698 following order:
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699
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700 - the **name of a column of `variableMetadata`** which must have numerical data (only letters, digits, periods, and underscores are permitted in the name itself), e.g., 'mz';
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701 - the **minimum allowed value** in that column for the feature to be retained, e.g., '200';
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702 - the **maximum allowed value**, e.g., '800'.
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703
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704 Note for the range specification strings:
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705
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706 - **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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707 - **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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708
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709 - 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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710
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711 -----------------------------------------------------------------------------
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712
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713 ----------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
714 WORKING EXAMPLES
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
715 ----------------
2
23c6d271def9 planemo upload
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diff changeset
716
23c6d271def9 planemo upload
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diff changeset
717 .. class:: infomark
23c6d271def9 planemo upload
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diff changeset
718
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
719 -----------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
720 Input Files
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
721 -----------
2
23c6d271def9 planemo upload
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diff changeset
722
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
723 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
724 | Input File URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
725 +======================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
726 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_dataMatrix.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
727 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
728 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_sampleMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
729 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
730 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_variableMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
731 +------------------------------------------------------------------------------------------------------------------------------------------------------+
2
23c6d271def9 planemo upload
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diff changeset
732
23c6d271def9 planemo upload
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diff changeset
733 .. class:: infomark
23c6d271def9 planemo upload
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diff changeset
734
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
735 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
736 Running Without Range-Filtering
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
737 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
738
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
739 This example retains only samples whose 'gender' attribute is 'M'.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
740
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
741 **Input parameters**
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
742
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
743 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
744 | Input Parameter | Value |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
745 +====================================+===============================+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
746 | Names of sample-classes | M |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
747 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
748 | Include named classes | filter-in |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
749 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
750 | Column that names the sample-class | gender |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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parents: 7
diff changeset
751 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
752 | Variable range-filters | (Leave this field empty.) |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
753 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
754 | Data transforamtion | none |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
755 +------------------------------------+-------------------------------+
2
23c6d271def9 planemo upload
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diff changeset
756
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
757 **Expected outputs**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
758
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
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diff changeset
759 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
760 | Expected Output | Download from URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
761 +===================+=================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
762 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_dataMatrix.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
763 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
764 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_sampleMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
765 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
766 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/expected_variableMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
767 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
768
2
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diff changeset
769 .. class:: infomark
23c6d271def9 planemo upload
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diff changeset
770
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
771 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
772 Running With Range-Filtering
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
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diff changeset
773 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
774
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
775 This example retains only features whose mz is greater than 200, whose rt is less than 800, and whose maximum intensity across all samples is 2,000,000.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
776 This example retains all samples (except those having zero variance for all feature), although it would be possible to filter on samples as well.
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
777
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
778 **Input parameters**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
779
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
780 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
781 | Input Parameter | Value |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
782 +====================================+====================================+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
783 | Names of sample-classes | (Leave this field empty.) |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
784 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
785 | Include named classes | filter-out |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
786 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
787 | Column that names the sample-class | gender |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
788 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
789 | Variable range-filters | FEATMAX:20.93157:,mz:200:,rt::800 |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
790 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
791 | Data transforamtion | log2 |
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
792 +------------------------------------+------------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
793
2
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diff changeset
794 **Expected outputs**
23c6d271def9 planemo upload
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diff changeset
795
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
796 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
797 | Expected Output | Download from URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
798 +===================+===================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
799 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_dataMatrix.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
800 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
801 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_sampleMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
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diff changeset
802 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
803 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
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diff changeset
804 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
805 ]]></help>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
806 <citations>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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807 <!-- Giacomoni_2014 W4m 2.5 -->
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808 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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809 <!-- Guitton_2017 W4m 3.0 -->
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810 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
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811 <!-- Kuhl_2012 CAMERA -->
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812 <citation type="doi">10.1021/ac202450g</citation>
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813 <!-- Smith_2006 XCMS -->
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814 <citation type="doi">10.1021/ac051437y</citation>
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815 <!-- Thevenot_2015 Urinary metabolome statistics -->
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816 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
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817 </citations>
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818 <!--
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819 vim:noet:sw=4:ts=4
3
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820 --> </tool>