Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 10:649cb1bafd3e draft

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planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
author eschen42
date Thu, 09 Aug 2018 13:00:51 -0400
parents 1ced8b5dfa3e
children 9f5c0e23c205
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10
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1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.10">
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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>
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8 <requirement type="package" version="0.98.7">w4mclassfilter</requirement>
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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="&#45;" /> <!-- dash, hyphen -->
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39 <add value="&#46;" /> <!-- dot, period -->
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40 <add value="&#95;" /> <!-- underscore -->
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41 </valid>
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42 </sanitizer>
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43 </param>
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44 <param name="sampleclassNames" label="Names of sample-classes" type="text" value = ""
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45 help="comma-separated names (or regular expressions to match names) of sample-classes to filter in or out; defaults to no names">
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46 <sanitizer>
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47 <valid initial="string.letters">
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48 <add preset="string.digits"/>
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49 <add value="&#123;" /> <!-- l-cube, left-curly-bracket -->
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50 <add value="&#124;" /> <!-- pipe -->
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51 <add value="&#125;" /> <!-- r-cube, right-curly-bracket -->
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52 <add value="&#36;" /> <!-- dollar, dollar-sign -->
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53 <add value="&#40;" /> <!-- left-paren -->
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54 <add value="&#41;" /> <!-- right-paren -->
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55 <add value="&#42;" /> <!-- splat, asterisk -->
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56 <add value="&#43;" /> <!-- plus -->
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57 <add value="&#45;" /> <!-- dash, hyphen -->
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58 <add value="&#44;" /> <!-- comma -->
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59 <add value="&#46;" /> <!-- dot, period -->
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60 <add value="&#58;" /> <!-- colon -->
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61 <add value="&#59;" /> <!-- semi, semicolon -->
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62 <add value="&#63;" /> <!-- what, question mark -->
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63 <add value="&#91;" /> <!-- l-squib, left-squre-bracket -->
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64 <add value="&#92;" /> <!-- whack, backslash -->
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65 <add value="&#93;" /> <!-- r-squib, right-squre-bracket -->
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66 <add value="&#94;" /> <!-- hat, caret -->
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67 <add value="&#95;" /> <!-- underscore -->
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68 </valid>
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69 </sanitizer>
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70 </param>
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71 <param name="wildcards" label="Use 'wild cards' or 'regular expressions'" type="select"
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72 help="'wild-cards' (the default) - use '*' and '?' to match class names; 'regular-expressions' - use regular expressions to match class names">
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73 <option value="TRUE" selected="true">wild-cards</option>
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74 <option value="FALSE">regular-expressions</option>
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75 </param>
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76 <param name="inclusive" label="Exclude/include named classes" type="select"
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77 help="'filter-out' (the default) - exclude only the named sample-classes; 'filter-in' - include only the named sample-classes">
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78 <option value="TRUE">filter-in</option>
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79 <option value="FALSE" selected="true">filter-out</option>
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80 </param>
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81 <param name="variableRangeFilter" label="Variable-range filters" type="text" value = ""
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82 help="comma-separated filters, each specified as 'variableMetadataColumnName:min:max'; default is no filters. (See help below.)">
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83 <sanitizer>
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84 <valid initial="string.letters">
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85 <add preset="string.digits"/>
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86 <add value="&#44;" /> <!-- comma -->
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87 <add value="&#45;" /> <!-- dash, hyphen -->
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88 <add value="&#46;" /> <!-- dot, period -->
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89 <add value="&#58;" /> <!-- colon -->
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90 <add value="&#95;" /> <!-- underscore -->
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91 </valid>
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92 </sanitizer>
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93 </param>
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94 <param name="transformation" label="Data-transformation" type="select"
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95 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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96 <option value="none" selected="true">none</option>
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97 <option value="log2">log2</option>
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98 <option value="log10">log10</option>
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99 </param>
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100 </inputs>
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101 <outputs>
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102 <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>
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103 <data name="sampleMetadata_out" format="tabular" label="${sampleMetadata_in.name}.subset" ></data>
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104 <data name="variableMetadata_out" format="tabular" label="${variableMetadata_in.name}.subset" ></data>
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105 </outputs>
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106 <tests>
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107 <!-- test 1 -->
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108 <test>
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109 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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110 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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111 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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112 <param name="classnameColumn" value="gender"/>
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113 <param name="sampleclassNames" value="M"/>
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114 <param name="wildcards" value="FALSE"/>
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115 <param name="inclusive" value="filter-in"/>
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116 <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
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117 <param name="transformation" value="log10"/>
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118 <output name="dataMatrix_out">
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119 <assert_contents>
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120 <has_text text="5.87336711011293" />
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121 </assert_contents>
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122 </output>
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123 <output name="sampleMetadata_out">
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124 <assert_contents>
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125 <not_has_text text="HU_028" />
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126 <not_has_text text="HU_051" />
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127 <not_has_text text="HU_060" />
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128 <not_has_text text="HU_110" />
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129 <not_has_text text="HU_149" />
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130 <not_has_text text="HU_152" />
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131 <not_has_text text="HU_175" />
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132 <not_has_text text="HU_178" />
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133 <not_has_text text="HU_185" />
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134 <not_has_text text="HU_204" />
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135 <not_has_text text="HU_208" />
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136 <has_text text="HU_017" />
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137 <has_text text="HU_034" />
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138 <has_text text="HU_078" />
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139 <has_text text="HU_091" />
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140 <has_text text="HU_093" />
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141 <has_text text="HU_099" />
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142 <has_text text="HU_130" />
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143 <has_text text="HU_134" />
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144 <has_text text="HU_138" />
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145 </assert_contents>
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146 </output>
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147 <output name="variableMetadata_out">
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148 <assert_contents>
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149 <not_has_text text="HMDB00191" />
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150 <has_text text="HMDB00208" />
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151 <not_has_text text="HMDB00251" />
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152 <not_has_text text="HMDB00299" />
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153 <not_has_text text="HMDB00512" />
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154 <not_has_text text="HMDB00518" />
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155 <not_has_text text="HMDB00715" />
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156 <not_has_text text="HMDB00822" />
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157 <has_text text="HMDB01032" />
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158 <has_text text="HMDB01101.1" />
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159 <not_has_text text="HMDB03193" />
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160 <not_has_text text="HMDB04824" />
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161 <not_has_text text="HMDB10348" />
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162 <has_text text="HMDB13189" />
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163 <not_has_text text="HMDB59717" />
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164 </assert_contents>
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165 </output>
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166 </test>
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167 <!-- test 2 -->
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168 <test>
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169 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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170 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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171 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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172 <param name="classnameColumn" value="sampleMetadata"/>
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173 <!-- test that hyphens in regular expressions work -->
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174 <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/>
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175 <param name="wildcards" value="FALSE"/>
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176 <param name="inclusive" value="filter-in"/>
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177 <param name="variableRangeFilter" value="FEATMAX:20.93157:,mz:200:,rt::800"/>
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178 <param name="transformation" value="log2"/>
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179 <output name="dataMatrix_out">
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180 <assert_contents>
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181 <has_text text="19.5109032146715" />
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182 </assert_contents>
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183 </output>
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184 <output name="sampleMetadata_out">
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185 <assert_contents>
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186 <has_text text="HU_028" />
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187 <has_text text="HU_051" />
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188 <has_text text="HU_060" />
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189 <has_text text="HU_110" />
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190 <has_text text="HU_149" />
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191 <has_text text="HU_152" />
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192 <has_text text="HU_175" />
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193 <has_text text="HU_178" />
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194 <has_text text="HU_185" />
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195 <not_has_text text="HU_204" />
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196 <has_text text="HU_208" />
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197 <has_text text="HU_017" />
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198 <has_text text="HU_034" />
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199 <has_text text="HU_078" />
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200 <has_text text="HU_091" />
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201 <has_text text="HU_093" />
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202 <has_text text="HU_099" />
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203 <has_text text="HU_130" />
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204 <has_text text="HU_134" />
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205 <has_text text="HU_138" />
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206 </assert_contents>
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207 </output>
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208 <output name="variableMetadata_out">
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209 <assert_contents>
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210 <has_text text="HMDB00191" />
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211 <has_text text="HMDB00208" />
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212 <not_has_text text="HMDB00251" />
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213 <not_has_text text="HMDB00299" />
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214 <not_has_text text="HMDB00512" />
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215 <not_has_text text="HMDB00518" />
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216 <not_has_text text="HMDB00715" />
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217 <not_has_text text="HMDB00822" />
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218 <has_text text="HMDB01032" />
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219 <has_text text="HMDB01101.1" />
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220 <not_has_text text="HMDB03193" />
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221 <not_has_text text="HMDB04824" />
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222 <not_has_text text="HMDB10348" />
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223 <has_text text="HMDB13189" />
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224 <not_has_text text="HMDB59717" />
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225 </assert_contents>
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226 </output>
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227 </test>
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228 <!-- test 3 -->
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229 <test>
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230 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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231 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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232 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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233 <param name="classnameColumn" value="gender"/>
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234 <param name="sampleclassNames" value="M"/>
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235 <param name="inclusive" value="filter-in"/>
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236 <param name="transformation" value="none"/>
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237 <output name="dataMatrix_out">
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238 <assert_contents>
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239 <not_has_text text="HU_028" />
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240 <not_has_text text="HU_051" />
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241 <not_has_text text="HU_060" />
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242 <not_has_text text="HU_110" />
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243 <not_has_text text="HU_149" />
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244 <not_has_text text="HU_152" />
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245 <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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246 <not_has_text text="HU_178" />
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247 <not_has_text text="HU_185" />
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248 <not_has_text text="HU_204" />
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249 <not_has_text text="HU_208" />
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250 <has_text text="HU_017" />
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251 <has_text text="HU_034" />
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252 <has_text text="HU_078" />
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253 <has_text text="HU_091" />
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254 <has_text text="HU_093" />
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255 <has_text text="HU_099" />
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256 <has_text text="HU_130" />
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257 <has_text text="HU_134" />
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258 <has_text text="HU_138" />
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259 <has_text text="HMDB03193" />
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260 <not_has_text text="HMDB00822" />
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261 <has_text text="HMDB01101" />
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262 <has_text text="HMDB01101.1" />
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263 <has_text text="HMDB10348" />
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264 <has_text text="HMDB59717" />
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265 <has_text text="HMDB13189" />
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266 <has_text text="HMDB00299" />
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267 <has_text text="HMDB00191" />
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268 <has_text text="HMDB00518" />
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269 <has_text text="HMDB00715" />
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270 <has_text text="HMDB01032" />
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271 <has_text text="HMDB00208" />
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272 <has_text text="HMDB04824" />
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273 <has_text text="HMDB00512" />
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274 <has_text text="HMDB00251" />
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275 </assert_contents>
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276 </output>
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277 </test>
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278 <!-- test 4 -->
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279 <test>
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280 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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281 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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282 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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283 <param name="classnameColumn" value="gender"/>
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284 <param name="sampleclassNames" value="*"/>
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285 <param name="wildcards" value="TRUE"/>
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286 <param name="inclusive" value="filter-in"/>
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287 <output name="sampleMetadata_out">
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288 <assert_contents>
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289 <not_has_text text="HU_204" />
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290 <has_text text="HU_028" />
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291 <has_text text="HU_051" />
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292 <has_text text="HU_060" />
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293 <has_text text="HU_110" />
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294 <has_text text="HU_149" />
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295 <has_text text="HU_152" />
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296 <has_text text="HU_175" />
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297 <has_text text="HU_178" />
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298 <has_text text="HU_185" />
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299 <has_text text="HU_208" />
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300 <has_text text="HU_017" />
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301 <has_text text="HU_034" />
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302 <has_text text="HU_078" />
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303 <has_text text="HU_091" />
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304 <has_text text="HU_093" />
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305 <has_text text="HU_099" />
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306 <has_text text="HU_130" />
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307 <has_text text="HU_134" />
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308 <has_text text="HU_138" />
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309 </assert_contents>
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310 </output>
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311 </test>
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312 <!-- test 5 -->
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313 <test>
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314 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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315 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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316 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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317 <param name="classnameColumn" value="gender"/>
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318 <param name="sampleclassNames" value="M"/>
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319 <param name="wildcards" value="FALSE"/>
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320 <param name="inclusive" value="filter-in"/>
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321 <output name="sampleMetadata_out">
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322 <assert_contents>
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323 <not_has_text text="HU_028" />
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324 <not_has_text text="HU_051" />
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325 <not_has_text text="HU_060" />
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326 <not_has_text text="HU_110" />
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327 <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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328 <not_has_text text="HU_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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329 <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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330 <not_has_text text="HU_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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331 <not_has_text text="HU_185" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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332 <not_has_text text="HU_204" />
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333 <not_has_text text="HU_208" />
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334 <has_text text="HU_017" />
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335 <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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336 <has_text text="HU_078" />
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337 <has_text text="HU_091" />
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338 <has_text text="HU_093" />
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339 <has_text text="HU_099" />
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340 <has_text text="HU_130" />
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341 <has_text text="HU_134" />
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342 <has_text text="HU_138" />
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343 </assert_contents>
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344 </output>
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345 </test>
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346 <!-- test 6 -->
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347 <test>
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348 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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349 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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350 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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351 <param name="classnameColumn" value="gender"/>
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352 <param name="sampleclassNames" value="M"/>
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353 <param name="wildcards" value="FALSE"/>
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354 <param name="inclusive" value="filter-in"/>
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355 <output name="variableMetadata_out">
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356 <assert_contents>
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357 <has_text text="HMDB03193" />
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358 <not_has_text text="HMDB00822" />
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359 <has_text text="HMDB01101" />
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360 <has_text text="HMDB01101.1" />
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361 <has_text text="HMDB10348" />
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362 <has_text text="HMDB59717" />
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363 <has_text text="HMDB13189" />
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364 <has_text text="HMDB00299" />
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365 <has_text text="HMDB00191" />
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366 <has_text text="HMDB00518" />
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367 <has_text text="HMDB00715" />
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368 <has_text text="HMDB01032" />
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369 <has_text text="HMDB00208" />
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370 <has_text text="HMDB04824" />
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371 <has_text text="HMDB00512" />
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372 <has_text text="HMDB00251" />
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373 </assert_contents>
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374 </output>
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375 </test>
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376 <!-- test 7 -->
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377 <test>
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378 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/>
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379 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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380 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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381 <param name="classnameColumn" value="gender"/>
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382 <param name="sampleclassNames" value="M"/>
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383 <param name="wildcards" value="FALSE"/>
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384 <param name="inclusive" value="filter-in"/>
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385 <output name="variableMetadata_out">
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386 <assert_contents>
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387 <has_text text="HMDB03193" />
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388 <not_has_text text="HMDB00822" />
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389 <has_text text="HMDB01101" />
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diff changeset
390 <has_text text="HMDB01101.1" />
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diff changeset
391 <has_text text="HMDB10348" />
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diff changeset
392 <has_text text="HMDB59717" />
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393 <not_has_text text="HMDB13189" />
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diff changeset
394 <has_text text="HMDB00299" />
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395 <has_text text="HMDB00191" />
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diff changeset
396 <has_text text="HMDB00518" />
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diff changeset
397 <has_text text="HMDB00715" />
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diff changeset
398 <has_text text="HMDB01032" />
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diff changeset
399 <has_text text="HMDB00208" />
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diff changeset
400 <has_text text="HMDB04824" />
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diff changeset
401 <has_text text="HMDB00512" />
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402 <has_text text="HMDB00251" />
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403 </assert_contents>
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404 </output>
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405 </test>
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406 <!-- test 8 -->
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407 <test>
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408 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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409 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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410 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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411 <param name="classnameColumn" value="gender"/>
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412 <param name="sampleclassNames" value="[Mm],[fF]"/>
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413 <param name="wildcards" value="FALSE"/>
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414 <param name="inclusive" value="filter-in"/>
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415 <output name="sampleMetadata_out">
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416 <assert_contents>
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417 <has_text text="HU_028" />
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418 <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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419 <has_text text="HU_060" />
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420 <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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421 <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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422 <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
423 <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
424 <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
425 <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
426 <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
427 <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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428 <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
429 <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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430 <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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431 <has_text text="HU_091" />
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432 <has_text text="HU_093" />
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433 <has_text text="HU_099" />
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434 <has_text text="HU_130" />
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435 <has_text text="HU_134" />
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436 <has_text text="HU_138" />
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437 </assert_contents>
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438 </output>
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439 </test>
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440 <!-- test 9 -->
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441 <test>
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442 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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443 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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444 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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445 <param name="classnameColumn" value=""/>
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446 <param name="sampleclassNames" value="M"/>
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447 <param name="wildcards" value="FALSE"/>
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448 <param name="inclusive" value="filter-in"/>
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449 <output name="sampleMetadata_out">
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450 <assert_contents>
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451 <has_text text="HU_028" />
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452 <has_text text="HU_051" />
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453 <has_text text="HU_060" />
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454 <has_text text="HU_110" />
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455 <has_text text="HU_149" />
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456 <has_text text="HU_152" />
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457 <has_text text="HU_175" />
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458 <has_text text="HU_178" />
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459 <has_text text="HU_185" />
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460 <not_has_text text="HU_204" />
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461 <has_text text="HU_208" />
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462 <has_text text="HU_017" />
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463 <has_text text="HU_034" />
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464 <has_text text="HU_078" />
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465 <has_text text="HU_091" />
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466 <has_text text="HU_093" />
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467 <has_text text="HU_099" />
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468 <has_text text="HU_130" />
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469 <has_text text="HU_134" />
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470 <has_text text="HU_138" />
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471 </assert_contents>
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472 </output>
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473 </test>
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474 </tests>
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475 <help><![CDATA[
0
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476
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477
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478 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
0
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479
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480 --------------------------------------------------------------------------
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481
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482
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483 **R package**
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484
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485 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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486
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487 -----------------------------------------------------------------------------------------------------------------------------------------
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488
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489
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490 **Tool updates**
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491
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492 See the **NEWS** section at the bottom of this page
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493
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494 ---------------------------------------------------
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495
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496 ===========================================================
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497 "W4m Data Subset" - Filter Workflow4Metabolomics data files
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498 ===========================================================
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499
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500 ----------
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501 Motivation
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502 ----------
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503
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504 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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505 (If the MS protocol includes fragmentation, several features may result for each chemical.)
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506 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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507 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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508
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509 The chromatographic retention-time for a chemical can vary from one chromatography run to the next.
8
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510 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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511 Features may be better aligned if pooled samples and blanks are included.
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512
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513 Multivariate statistical techniques may be used to discover clusters of similar samples (Th]]>&#233;<![CDATA[venot *et al.*, 2015).
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514 However, once retention-time alignment of features has been achieved among samples in GC-MS and LC-MS datasets:
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515
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516 - The presence of pools and blanks may confound identification and separation of clusters.
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517 - Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance.
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518
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519 -----------
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520 Description
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521 -----------
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522
8
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523 The **W4m Data Subset** tool **selects subsets of samples, features, or data values** for further analysis.
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524
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525 - 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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526 - The tool produces the same trio of output datasets, modified as follows.
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527
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528 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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529
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530 - Samples may be eliminated by filtering on a designated “sample class” column in sampleMetadata.
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531 - Features may be eliminated by specifying minimum or maximum value (or both) allowable in columns of variableMetadata.
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532 - 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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533
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534 This tool also performs several operations to address several data issues that may impede downstream statistical analysis:
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535
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536 - Missing values in dataMatrix are imputed to zero.
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537 - The values in the dataMatrix may be log-transformed if desired.
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538 - Samples that are missing from either sampleMetadata or dataMatrix are eliminated.
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539 - Features that are missing from either variableMetadata or dataMatrix are eliminated.
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540 - Features and samples that have zero variance are eliminated.
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541 - Samples and features are sorted alphabetically in rows and columns of dataMatrix and in rows of variableMetadata and sampleMetadata.
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542 - The names of the first columns of variableMetadata and sampleMetadata are set respectively to "variableMetadata" and "sampleMetadata".
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543
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544 This tool may be applied several times sequentially, which may be useful for:
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545
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546 - analyzing subsets of samples for progressively smaller sets of treatment-levels, or
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547 - choosing subsets of samples based on criteria in several columns of the sampleMetadata table.
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548
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549 -----------------
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550 Workflow Position
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551 -----------------
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552
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553 This tool can be used at any point downstream of Preprocessing.
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554
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555 - Possible upstream tool categories: Preprocessing, Quality Control, Statistical Analysis, Filter and Sort
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556 - Possible downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
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557
0
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558 -----------
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559 Input files
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560 -----------
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561
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562 +---------------------------+------------+
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563 | File | Format |
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564 +===========================+============+
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565 | Data matrix | tabular |
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566 +---------------------------+------------+
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567 | Sample metadata | tabular |
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568 +---------------------------+------------+
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569 | Variable metadata | tabular |
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570 +---------------------------+------------+
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571
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572
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573 ----------
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574 Parameters
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575 ----------
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576
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577 Data matrix file
8
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578 | 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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579 |
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580
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581 Sample metadata file
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582 | 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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583 |
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584
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585 Variable metadata file
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586 | 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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587 |
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588
8
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589 Column that names the sample-class (default = '``class``')
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590 | name of the column in **sampleMetadata** that has the values to be tested against the '``Names of sample-classes``' input parameter
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591 |
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592
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593 Names of sample-classes (default = no names)
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594 | comma-separated names (or regular expressions to match names) of sample-classes to include or exclude
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595 |
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596
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597 'Wild cards' or 'regular expressions' (default = '``wild-cards``')
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598 | '``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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599 | '``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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600 |
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601
8
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602 Exclude/include named classes (default = '``filter-out``')
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603 | '``filter-in``' - include only the named sample-classes
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604 | '``filter-out``' - exclude only the named sample-classes
0
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605 |
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606
6
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607 Variable-range filters (default = no filters)
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608 | comma-separated names of variable-range filters (see the 'Variable-range filters' section below)
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609 |
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610
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611 Data-transformation (default = '``none``')
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612 | '``none``' - do not transform data matrix values
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613 | '``log2``' - take the log base 2 of the values in the data matrix
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614 | '``log10``' - take the log base 10 of the values in the data matrix
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615 | In both cases, negative and missing values are imputed to zero.
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616 |
0
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617
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618
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619 ------------
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620 Output files
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621 ------------
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622
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623 sampleMetadata
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624 | (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples that have been filtered out (by the sample-class filter, or because of zero variance, or because they were missing in the input data matrix)
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625 |
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626
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627 variableMetadata
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628 | (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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629 |
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630
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631 dataMatrix
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632 | (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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633 |
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634
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635
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636 -----------------------------------------
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637 'Wild card' patterns to match class-names
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638 -----------------------------------------
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639
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640 W4m Data Subset supports use of R "wild card" patterns to select class-names.
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641
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642 - use '``?``' to match a single character
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643 - use '``*``' to match zero or more characters
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644 - the entire pattern must match the sample name
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645
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646 For example
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647
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648 - '``??.samp*``' matches '``my.sample``' but not '``my.own.sample``'
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649 - '``*.sample``' matches '``my.sample``' and '``my.own.sample``'
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650 - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``'
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651
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652 --------------------------------------------------
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653 'Regular expression' patterns to match class-names
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654 --------------------------------------------------
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655
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656 W4m Data Subset supports use of R "regular expression" patterns to select class-names.
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657
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658 R uses POSIX 1003.2 standard regular expressions, which allow precise pattern-matching and are exhaustively defined at:
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659 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
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660
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661 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
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662
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663 - '``^``' matches the beginning of a class-name
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664 - '``$``' matches the end of a class-name
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665 - '``.``' outside of square brackets matches a single character
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666 - '``*``' matches character specified immediately before zero or more times
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667 - square brackets specify a set of characters to be matched.
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668
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669 Within square brackets
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670
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671 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
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672 - '``-``' is used to specify ranges of characters
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673
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674 Caveat: The tool wrapper uses the comma ('``,``') to split a list of sample-class names, so **commas may not be used within regular expressions for this tool**
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675
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676 First Example: Consider a field of class-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
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677
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678 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
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679 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
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680 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
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681 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-classes as '``front3,front6,front9,marq3,marq6,marq9``'
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682
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683 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
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684
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685 - '``^[A-Z][A-Z][0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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686 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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687 - '``^[A-Z][0-9]*``' - MATCHES '``**^A** B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
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688 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
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689 - '``^[A-Z][A-Z]*[0-9][0-9]$``' - NO MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
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690 - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
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691
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692 ----------------------
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693 Variable-range filters
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694 ----------------------
4
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695
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696 An array of range-specification strings may be supplied in the `variableRangeFilter`
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697 argument. If supplied, only features having numerical values in the specified column
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698 of `variableMetadata` that fall within the specified ranges will be retained
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699 in the output. Each range is a string of three colon-separated values (e.g., "mz:200:800") in the
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700 following order:
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701
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702 - the **name of a column of `variableMetadata`** which must have numerical data (e.g., "mz");
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703 - the **minimum allowed value** in that column for the feature to be retained (e.g., 200);
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704 - the **maximum allowed value** (e.g., 800).
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705
10
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706 Note for the range specification strings:
6
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707
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708 - **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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709 - **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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710
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711 - 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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diff changeset
712
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
713 -----------------------------------------------------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
714
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
715 ----------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
716 WORKING EXAMPLES
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
717 ----------------
2
23c6d271def9 planemo upload
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diff changeset
718
23c6d271def9 planemo upload
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diff changeset
719 .. class:: infomark
23c6d271def9 planemo upload
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diff changeset
720
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
721 -----------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
722 Input Files
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
723 -----------
2
23c6d271def9 planemo upload
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diff changeset
724
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
725 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
726 | Input File URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
727 +======================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
728 | 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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parents: 9
diff changeset
729 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
730 | 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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parents: 9
diff changeset
731 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
732 | 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
733 +------------------------------------------------------------------------------------------------------------------------------------------------------+
2
23c6d271def9 planemo upload
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diff changeset
734
23c6d271def9 planemo upload
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diff changeset
735 .. class:: infomark
23c6d271def9 planemo upload
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diff changeset
736
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
737 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
738 Running Without Range-Filtering
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
739 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
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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parents: 5
diff changeset
741 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
742
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
743 **Input parameters**
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
744
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
745 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
746 | 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
747 +====================================+===============================+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
748 | 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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parents: 7
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 | 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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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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parents: 7
diff changeset
752 | 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
753 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
754 | 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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parents: 7
diff changeset
755 +------------------------------------+-------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
756 | 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
757 +------------------------------------+-------------------------------+
2
23c6d271def9 planemo upload
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diff changeset
758
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
759 **Expected outputs**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
760
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
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 | 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
763 +===================+=================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
764 | 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
765 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
766 | 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
767 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
768 | 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
769 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
770
2
23c6d271def9 planemo upload
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diff changeset
771 .. class:: infomark
23c6d271def9 planemo upload
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diff changeset
772
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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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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diff changeset
774 Running With Range-Filtering
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
775 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
776
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
777 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
778 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
779
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
780 **Input parameters**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
781
8
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 | 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
784 +====================================+====================================+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
785 | 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
786 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
787 | 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
788 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
789 | 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
790 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
791 | 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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parents: 7
diff changeset
792 +------------------------------------+------------------------------------+
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
793 | 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
794 +------------------------------------+------------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
795
2
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diff changeset
796 **Expected outputs**
23c6d271def9 planemo upload
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diff changeset
797
10
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 | 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
800 +===================+===================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
801 | 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
eschen42
parents: 9
diff changeset
802 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
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diff changeset
803 | 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
parents: 9
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 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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806 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
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807 ]]></help>
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808 <citations>
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809 <!-- Giacomoni_2014 W4m 2.5 -->
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810 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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811 <!-- Guitton_2017 W4m 3.0 -->
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812 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
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813 <!-- Kuhl_2012 CAMERA -->
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814 <citation type="doi">10.1021/ac202450g</citation>
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815 <!-- Smith_2006 XCMS -->
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816 <citation type="doi">10.1021/ac051437y</citation>
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817 <!-- Thevenot_2015 Urinary metabolome statistics -->
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818 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
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819 </citations>
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820 <!--
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821 vim:noet:sw=4:ts=4
3
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822 --> </tool>