Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 5:2cdf7d5982c8 draft

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planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
author eschen42
date Thu, 07 Sep 2017 17:41:09 -0400
parents 499c7ecfa834
children 38ccf6722d54
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1 <tool id="w4mclassfilter" name="Sample_Subset" version="0.98.3">
0
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2 <description>Filter W4M data by sample class</description>
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3
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4 <requirements>
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5 <requirement type="package" version="3.3.2">r-base</requirement>
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6 <requirement type="package" version="1.1_4">r-batch</requirement>
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7 <requirement type="package" version="0.98.3">w4mclassfilter</requirement>
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8 </requirements>
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9
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10 <stdio>
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11 <exit_code range="1:" level="fatal" />
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12 </stdio>
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13
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14
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15 <command detect_errors="aggressive"><![CDATA[
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16 Rscript $__tool_directory__/w4mclassfilter_wrapper.R
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17 dataMatrix_in '$dataMatrix_in'
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18 sampleMetadata_in '$sampleMetadata_in'
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19 variableMetadata_in '$variableMetadata_in'
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20 sampleclassNames '$sampleclassNames'
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21 inclusive '$inclusive'
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22 wildcards '$wildcards'
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23 classnameColumn '$classnameColumn'
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24 samplenameColumn '$samplenameColumn'
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25 dataMatrix_out '$dataMatrix_out'
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26 sampleMetadata_out '$sampleMetadata_out'
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27 variableMetadata_out '$variableMetadata_out'
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28 ]]></command>
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29
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30 <inputs>
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31 <param name="dataMatrix_in" label="Data matrix file" type="data" format="tabular" help="variable x sample, decimal: '.', missing: NA, mode: numerical, separator: tab" />
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32 <param name="sampleMetadata_in" label="Sample metadata file" type="data" format="tabular" help="sample x metadata columns, separator: tab" />
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33 <param name="variableMetadata_in" label="Variable metadata file" type="data" format="tabular" help="variable x metadata columns, separator: tab" />
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34 <param name="samplenameColumn" label="Column that names the sample" type="text" value = "sampleMetadata" help="name of the column in the sample metadata file that has the name of the sample - defaults to 'sampleMetadata'" />
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35 <param name="classnameColumn" label="Column that names the sample-class" type="text" value = "class" help="name of the column in sample metadata that has the values to be tested against the 'classes' input parameter - defaults to 'class'" />
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36 <param name="sampleclassNames" label="Names of sample classes" type="text" value = "" help="comma-separated names (or comma-less regular expressions to match names) of sample-classes to filter in or out; defaults to no names">
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37 <sanitizer>
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38 <valid initial="string.letters">
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39 <add preset="string.digits"/>
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40 <add value="&#36;" /> <!-- dollar, dollar-sign -->
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41 <add value="&#40;" /> <!-- left-paren -->
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42 <add value="&#41;" /> <!-- right-paren -->
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43 <add value="&#42;" /> <!-- splat, asterisk -->
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44 <add value="&#43;" /> <!-- plus -->
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45 <add value="&#44;" /> <!-- comma -->
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46 <add value="&#46;" /> <!-- dot, period -->
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47 <add value="&#58;" /> <!-- colon -->
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48 <add value="&#59;" /> <!-- semi, semicolon -->
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49 <add value="&#63;" /> <!-- what, question mark -->
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50 <add value="&#91;" /> <!-- l-squib, left-squre-bracket -->
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51 <add value="&#92;" /> <!-- whack, backslash -->
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52 <add value="&#93;" /> <!-- r-squib, right-squre-bracket -->
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53 <add value="&#94;" /> <!-- hat, caret -->
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54 <add value="&#123;" /> <!-- l-cube, left-curly-bracket -->
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55 <add value="&#124;" /> <!-- pipe -->
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56 <add value="&#125;" /> <!-- r-cube, right-curly-bracket -->
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57 </valid>
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58 </sanitizer>
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59
4
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60 </param>
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61 <param name="wildcards" label="Use wild-cards or regular-expressions" type="select" help="wild-cards (the default) - use '*' and '?' to match class names; regular-expressions - use comma-less regular expressions to match class names">
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62 <option value="TRUE" selected="true">wild-cards</option>
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63 <option value="FALSE">regular-expressions</option>
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64 </param>
0
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65 <param name="inclusive" label="Include named classes" type="select" help="filter-in - include only the named sample classes; filter-out (the default) - exclude only the named sample classes">
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66 <option value="TRUE">filter-in</option>
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67 <option value="FALSE" selected="true">filter-out</option>
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68 </param>
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69 </inputs>
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70 <outputs>
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71 <data name="dataMatrix_out" label="${tool.name}_${dataMatrix_in.name}" format="tabular" ></data>
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72 <data name="sampleMetadata_out" label="${tool.name}_${sampleMetadata_in.name}" format="tabular" ></data>
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73 <data name="variableMetadata_out" label="${tool.name}_${variableMetadata_in.name}" format="tabular" ></data>
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74 </outputs>
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75
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76 <tests>
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77 <test>
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78 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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79 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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80 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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81 <param name="classnameColumn" value="gender"/>
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82 <param name="sampleclassNames" value="M"/>
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83 <param name="samplenameColumn" value="sampleMetadata"/>
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84 <param name="inclusive" value="filter-in"/>
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85 <output name="dataMatrix_out">
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86 <assert_contents>
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87 <not_has_text text="HU_028" />
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88 <not_has_text text="HU_051" />
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89 <not_has_text text="HU_060" />
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90 <not_has_text text="HU_110" />
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91 <not_has_text text="HU_149" />
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92 <not_has_text text="HU_152" />
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93 <not_has_text text="HU_175" />
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94 <not_has_text text="HU_178" />
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95 <not_has_text text="HU_185" />
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96 <not_has_text text="HU_204" />
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97 <not_has_text text="HU_208" />
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parents:
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98 <has_text text="HU_017" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
diff changeset
99 <has_text text="HU_034" />
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parents:
diff changeset
100 <has_text text="HU_078" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
diff changeset
101 <has_text text="HU_091" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
diff changeset
102 <has_text text="HU_093" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
diff changeset
103 <has_text text="HU_099" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
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104 <has_text text="HU_130" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
diff changeset
105 <has_text text="HU_134" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
106 <has_text text="HU_138" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
diff changeset
107 <has_text text="HMDB03193" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
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108 <not_has_text text="HMDB00822" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
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109 <has_text text="HMDB01101" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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110 <has_text text="HMDB01101.1" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
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111 <has_text text="HMDB10348" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
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112 <has_text text="HMDB59717" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
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113 <has_text text="HMDB13189" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
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114 <has_text text="HMDB00299" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
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115 <has_text text="HMDB00191" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
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116 <has_text text="HMDB00518" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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parents:
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117 <has_text text="HMDB00715" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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118 <has_text text="HMDB01032" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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119 <has_text text="HMDB00208" />
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120 <has_text text="HMDB04824" />
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parents:
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121 <has_text text="HMDB00512" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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122 <has_text text="HMDB00251" />
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123 </assert_contents>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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124 </output>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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125 </test>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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126 <test>
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127 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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128 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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129 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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130 <param name="classnameColumn" value="gender"/>
5
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131 <param name="sampleclassNames" value="*"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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132 <param name="wildcards" value="TRUE"/>
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133 <param name="samplenameColumn" value="sampleMetadata"/>
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134 <param name="inclusive" value="filter-in"/>
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135 <output name="sampleMetadata_out">
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136 <assert_contents>
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137 <not_has_text text="HU_204" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
138 <has_text text="HU_028" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
139 <has_text text="HU_051" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
140 <has_text text="HU_060" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
141 <has_text text="HU_110" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
142 <has_text text="HU_149" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
143 <has_text text="HU_152" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
144 <has_text text="HU_175" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
145 <has_text text="HU_178" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
146 <has_text text="HU_185" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
147 <has_text text="HU_208" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
148 <has_text text="HU_017" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
149 <has_text text="HU_034" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
150 <has_text text="HU_078" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
151 <has_text text="HU_091" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
152 <has_text text="HU_093" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
153 <has_text text="HU_099" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
154 <has_text text="HU_130" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
155 <has_text text="HU_134" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
156 <has_text text="HU_138" />
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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diff changeset
157 </assert_contents>
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158 </output>
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159 </test>
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diff changeset
160 <test>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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161 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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162 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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163 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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164 <param name="classnameColumn" value="gender"/>
0
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165 <param name="sampleclassNames" value="M"/>
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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166 <param name="wildcards" value="FALSE"/>
0
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167 <param name="samplenameColumn" value="sampleMetadata"/>
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168 <param name="inclusive" value="filter-in"/>
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169 <output name="sampleMetadata_out">
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170 <assert_contents>
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171 <not_has_text text="HU_028" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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172 <not_has_text text="HU_051" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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173 <not_has_text text="HU_060" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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174 <not_has_text text="HU_110" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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175 <not_has_text text="HU_149" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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176 <not_has_text text="HU_152" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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177 <not_has_text text="HU_175" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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178 <not_has_text text="HU_178" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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179 <not_has_text text="HU_185" />
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180 <not_has_text text="HU_204" />
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181 <not_has_text text="HU_208" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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182 <has_text text="HU_017" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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183 <has_text text="HU_034" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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184 <has_text text="HU_078" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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185 <has_text text="HU_091" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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186 <has_text text="HU_093" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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187 <has_text text="HU_099" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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188 <has_text text="HU_130" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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189 <has_text text="HU_134" />
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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190 <has_text text="HU_138" />
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191 </assert_contents>
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192 </output>
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193 </test>
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194 <test>
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195 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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196 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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197 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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198 <param name="classnameColumn" value="gender"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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199 <param name="sampleclassNames" value="M"/>
5
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200 <param name="wildcards" value="FALSE"/>
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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201 <param name="samplenameColumn" value="sampleMetadata"/>
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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202 <param name="inclusive" value="filter-in"/>
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203 <output name="variableMetadata_out">
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204 <assert_contents>
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205 <has_text text="HMDB03193" />
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206 <not_has_text text="HMDB00822" />
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207 <has_text text="HMDB01101" />
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208 <has_text text="HMDB01101.1" />
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209 <has_text text="HMDB10348" />
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210 <has_text text="HMDB59717" />
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211 <has_text text="HMDB13189" />
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212 <has_text text="HMDB00299" />
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213 <has_text text="HMDB00191" />
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214 <has_text text="HMDB00518" />
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215 <has_text text="HMDB00715" />
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216 <has_text text="HMDB01032" />
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217 <has_text text="HMDB00208" />
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218 <has_text text="HMDB04824" />
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219 <has_text text="HMDB00512" />
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220 <has_text text="HMDB00251" />
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221 </assert_contents>
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222 </output>
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223 </test>
4
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224 <test>
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225 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/>
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226 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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227 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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228 <param name="classnameColumn" value="gender"/>
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229 <param name="sampleclassNames" value="M"/>
5
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230 <param name="wildcards" value="FALSE"/>
4
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231 <param name="samplenameColumn" value="sampleMetadata"/>
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232 <param name="inclusive" value="filter-in"/>
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233 <output name="variableMetadata_out">
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234 <assert_contents>
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235 <has_text text="HMDB03193" />
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236 <not_has_text text="HMDB00822" />
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237 <has_text text="HMDB01101" />
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238 <has_text text="HMDB01101.1" />
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239 <has_text text="HMDB10348" />
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240 <has_text text="HMDB59717" />
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241 <not_has_text text="HMDB13189" />
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242 <has_text text="HMDB00299" />
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243 <has_text text="HMDB00191" />
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244 <has_text text="HMDB00518" />
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245 <has_text text="HMDB00715" />
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246 <has_text text="HMDB01032" />
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247 <has_text text="HMDB00208" />
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248 <has_text text="HMDB04824" />
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249 <has_text text="HMDB00512" />
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250 <has_text text="HMDB00251" />
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251 </assert_contents>
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252 </output>
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253 </test>
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254 <test>
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255 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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256 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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257 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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258 <param name="classnameColumn" value="gender"/>
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259 <param name="sampleclassNames" value="[Mm],[fF]"/>
5
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260 <param name="wildcards" value="FALSE"/>
4
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261 <param name="samplenameColumn" value="sampleMetadata"/>
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262 <param name="inclusive" value="filter-in"/>
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263 <output name="sampleMetadata_out">
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264 <assert_contents>
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265 <has_text text="HU_028" />
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266 <has_text text="HU_051" />
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267 <has_text text="HU_060" />
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268 <has_text text="HU_110" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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269 <has_text text="HU_149" />
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270 <has_text text="HU_152" />
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271 <has_text text="HU_175" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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272 <has_text text="HU_178" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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273 <has_text text="HU_185" />
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274 <not_has_text text="HU_204" />
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275 <has_text text="HU_208" />
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276 <has_text text="HU_017" />
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277 <has_text text="HU_034" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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278 <has_text text="HU_078" />
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279 <has_text text="HU_091" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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280 <has_text text="HU_093" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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281 <has_text text="HU_099" />
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282 <has_text text="HU_130" />
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283 <has_text text="HU_134" />
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284 <has_text text="HU_138" />
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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285 </assert_contents>
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286 </output>
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287 </test>
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288 <test>
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289 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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290 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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291 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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292 <param name="classnameColumn" value=""/>
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293 <param name="sampleclassNames" value="M"/>
5
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294 <param name="wildcards" value="FALSE"/>
4
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295 <param name="samplenameColumn" value="sampleMetadata"/>
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296 <param name="inclusive" value="filter-in"/>
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297 <output name="sampleMetadata_out">
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298 <assert_contents>
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299 <has_text text="HU_028" />
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300 <has_text text="HU_051" />
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301 <has_text text="HU_060" />
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302 <has_text text="HU_110" />
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303 <has_text text="HU_149" />
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304 <has_text text="HU_152" />
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305 <has_text text="HU_175" />
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306 <has_text text="HU_178" />
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307 <has_text text="HU_185" />
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308 <not_has_text text="HU_204" />
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309 <has_text text="HU_208" />
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310 <has_text text="HU_017" />
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311 <has_text text="HU_034" />
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312 <has_text text="HU_078" />
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313 <has_text text="HU_091" />
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314 <has_text text="HU_093" />
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315 <has_text text="HU_099" />
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316 <has_text text="HU_130" />
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317 <has_text text="HU_134" />
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318 <has_text text="HU_138" />
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319 </assert_contents>
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320 </output>
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321 </test>
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322 </tests>
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323
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324
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325
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326 <help><![CDATA[
0
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327
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328
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329 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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330
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331 --------------------------------------------------------------------------
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332
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333
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334 **R package**
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335
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336 The *w4mclassfilter* package is available from the Hegeman lab github repository (https://github.com/HegemanLab/w4mclassfilter/releases).
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337
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338 -----------------------------------------------------------------------------------------------------------------------------------------
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339
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340
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341 **Tool updates**
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342
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343 See the **NEWS** section at the bottom of this page
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344
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345 ---------------------------------------------------
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346
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347 ==============================================
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348 Filter Workflow4Metabolomics data matrix files
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349 ==============================================
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350
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351 -----------
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352 Description
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353 -----------
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354
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355 Filter a set of retention-corrected W4M files (dataMatrix, sampleMetadata, variableMetadata) by sample-class
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356
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357 -----------------
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358 Workflow Position
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359 -----------------
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360
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361 - Upstream tool category: Preprocessing
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362 - Downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
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363
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364 ----------
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365 Motivation
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366 ----------
0
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367
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368 GC-MS1 and LC-MS1 experiments seek to resolve chemicals as features that have distinct chromatographic behavior and (after ionization) mass-to-charge ratio.
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369 Data for a sample are collected as MS intensities, each of which is associated with a position on a 2D plane with dimensions of m/z ratio and chromatographic retention time.
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370 Ideally, features would be sufficiently reproducible from sample-run to sample-run to identify features that are commmon among samples and those that differ.
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371 However, the chromatographic retention time for a chemical can vary from one run to another.
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372 In the Workflow4Metabolomics (W4M, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017]) "flavor" of Galaxy, the XCMS [Smith *et al.*, 2006] preprocessing tools provide for "retention time correction" to align features among samples, but features may be better aligned if pooled samples and blanks are included.
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373
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374 Multivariate statistical techniques may be used to discover clusters of similar samples, and sometimes it is desirable to apply clustering iteratively to smaller and smaller subsets of samples until observable separation of clusters is no longer significant.
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375 Once feature-alignment has been achieved among samples in GC-MS and LC-MS datasets, however, the presence of pools and blanks may confound identification and separation of clusters.
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376 Multivariate statistical algorithms also may be impacted by missing values or dimensions that have zero variance (Thévenot *et al.*, 2015).
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377
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378 The w4mclassfilter tool provides a way to choose subsets of samples for further analysis.
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379 The tool takes as input the data matrix, sample metadata, and variable metadata Galaxy datasets produced by W4M and produces the same trio of datasets with data only for the selected samples.
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380 The tool uses a "sample-class" column in the sample metadata as the basis for including or eliminating samples for further analysis.
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381 Class-values to be considered are provided by the user as a comma-separated list.
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382 The user also provides an indication whether the list specifies classes to be included in further analysis ("filter-in") or rather to be excluded from it ("filter-out").
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383 Next, missing and negative intensites for features of the remaining samples are imputed to zero.
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384 Finally, samples or features with zero variance are eliminated.
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385
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386 -----------
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387 Input files
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388 -----------
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389
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390 +---------------------------+------------+
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391 | File | Format |
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392 +===========================+============+
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393 | Data matrix | tabular |
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394 +---------------------------+------------+
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395 | Sample metadata | tabular |
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396 +---------------------------+------------+
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397 | Variable metadata | tabular |
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398 +---------------------------+------------+
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399
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400
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401 ----------
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402 Parameters
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403 ----------
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404
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405 Data matrix file
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406 | variable x sample **dataMatrix** (tabular separated values) file of the numeric data matrix, with . as decimal, and NA for missing values; the table must not contain metadata apart from row and column names; the row and column names must be identical to the rownames of the sample and variable metadata, respectively (see below)
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407 |
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408
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409 Sample metadata file
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410 | sample x metadata **sampleMetadata** (tabular separated values) file of the numeric and/or character sample metadata, with . as decimal and NA for missing values
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411 |
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412
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413 Variable metadata file
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414 | 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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415 |
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416
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417 Column that names the sample (default = '``sampleMetadata``')
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418 | name of the column in sample metadata that has the name of the sample
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419 |
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420
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421 Column that names the sample-class (default = '``class``')
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422 | name of the column in sample metadata that has the values to be tested against the '``classes``' input parameter
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423 |
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424
0
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425 Names of sample classes (default = no names)
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426 | comma-separated names of sample classes to include or exclude
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427 |
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428
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429 Wild-cards (default = '``wild-cards``')
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430 | '``wild-cards``' - use wild-cards to match names of sample classes (see 'Wild card patterns to match class-names' below)
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431 | '``regular-expressions``' - exclude only the named sample classes (see 'Regular expression patterns to match class-names' below)
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432 |
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433
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434 Include named classes (default = '``filter-out``')
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435 | '``filter-in``' - include only the named sample classes
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436 | '``filter-out``' - exclude only the named sample classes
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437 |
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438
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439
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440
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441 ------------
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442 Output files
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443 ------------
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444
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445
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446 sampleMetadata
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447 | (tabular separated values) file identical to the **sampleMetadata** file given as an input argument, excepting lacking rows for samples (xC-MS features) that have been filtered out (by the sample-class filter or because of zero variance)
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448 |
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449
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450 variableMetadata
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451 | (tabular separated values) file identical to the **variableMetadata** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance)
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452 |
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453
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454 dataMatrix
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455 | (tabular separated values) file identical to the **dataMatrix** file given as an input argument, excepting lacking rows for variables (xC-MS features) that have been filtered out (because of zero variance) and columns that have been filtered out (by the sample-class filter or because of zero variance)
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456 |
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457
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458
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459 ---------------------------------------
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460 Wild card patterns to match class-names
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461 ---------------------------------------
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462
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463 Beginning with v0.98.2, w4mclassfilter supports use of R "wild card" patterns to select class-names.
4
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464
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465 - use '``?``' to match a single character
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466 - use '``*``' to match zero or more characters
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467 - the entire pattern must match the sample name
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468
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469 For example
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470
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471 - '``??.samp*``' matches '``my.sample``' but not '``my.own.sample``'
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472 - '``*.sample``' matches '``my.sample``' and '``my.own.sample``'
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473 - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``'
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474
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475 ------------------------------------------------
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476 Regular expression patterns to match class-names
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477 ------------------------------------------------
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478
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479 Beginning with v0.98.2, w4mclassfilter supports use of R "regular expression" patterns to select class-names.
4
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480
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481 R uses POSIX 1003.2 standard regular expressions, which allow precise pattern-matching and are exhaustively defined at:
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482 http://pubs.opengroup.org/onlinepubs/9699919799/basedefs/V1_chap09.html
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483
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484 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
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485
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486 - '``^``' matches the beginning of a class-name
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487 - '``$``' matches the end of a class-name
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488 - '``.``' outside of square brackets matches a single character
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489 - '``*``' matches character specified immediately before zero or more times
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490 - square brackets specify a set of characters to be matched.
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491
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492 Within square brackets
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493
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494 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
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495 - '``-``' is used to specify ranges of characters
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496
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497 Caveat: The tool wrapper uses the comma ('``,``') to split a list of sample-class names, so **commas may not be used within regular expressions for this tool**
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498
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499 First Example: Consider a field of class-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
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500
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501 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
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502 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
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503 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
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504 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-classes as '``front3,front6,front9,marq3,marq6,marq9``'
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505
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506 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
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507
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508 - '``^[A-Z][A-Z][0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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509 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' - MATCHES '``**^AB0123$**``'
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510 - '``^[A-Z][0-9]*``' - MATCHES '``**^A** B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
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511 - '``^[A-Z][A-Z][0-9]``' - MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
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512 - '``^[A-Z][A-Z]*[0-9][0-9]$``' - NO MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
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513 - '``^[A-Z][0-9]*$``' - NO MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
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514
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515
2
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516 ---------------
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517 Working example
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518 ---------------
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519
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520 .. class:: infomark
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521
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522 **Input files**
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523
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524 +-------------------+--------------------------------------------------------------------------------------------------------------+
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525 | Input File | Download from URL |
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526 +===================+==============================================================================================================+
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527 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_dataMatrix.tsv |
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528 +-------------------+--------------------------------------------------------------------------------------------------------------+
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529 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_sampleMetadata.tsv |
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530 +-------------------+--------------------------------------------------------------------------------------------------------------+
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531 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/input_variableMetadata.tsv |
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532 +-------------------+--------------------------------------------------------------------------------------------------------------+
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533
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534 .. class:: infomark
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535
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536 **Other input parameters**
0
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537
2
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538 +------------------------------------+-----------------+
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539 | Input Parameter | Value |
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540 +====================================+=================+
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541 | Names of sample classes | M |
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542 +------------------------------------+-----------------+
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543 | Include named classes | filter-in |
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544 +------------------------------------+-----------------+
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545 | Column that names the sample-class | gender |
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546 +------------------------------------+-----------------+
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547 | Column that names the sample | sampleMetadata |
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548 +------------------------------------+-----------------+
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549
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550 .. class:: infomark
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551
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552 **Expected outputs**
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553
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554 +-------------------+-----------------------------------------------------------------------------------------------------------------+
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555 | Expected Output | Download from URL |
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556 +===================+=================================================================================================================+
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557 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_dataMatrix.tsv |
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558 +-------------------+-----------------------------------------------------------------------------------------------------------------+
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559 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_sampleMetadata.tsv |
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560 +-------------------+-----------------------------------------------------------------------------------------------------------------+
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561 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/expected_variableMetadata.tsv |
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562 +-------------------+-----------------------------------------------------------------------------------------------------------------+
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563
0
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564
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565 -----------------------------------------------------------------------------
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566
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567 ----
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568 NEWS
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569 ----
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570
5
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571 CHANGES IN VERSION 0.98.3
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572 =========================
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573
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574 INTERNAL MODIFICATIONS
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575
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576 * Improved input handling.
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577 * Now uses w4mclassfilter R package v0.98.3, although that version has no functional implications for this tool.
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578 * Improved reference-list.
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579
4
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580 CHANGES IN VERSION 0.98.2
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581 =========================
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582
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583 NEW FEATURES
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584
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585 * Added support for R-flavored regular expression pattern-matching when selecting names of sample-classes.
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586 * Empty classes argument or zero-length class_column result in no samples filtered out.
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587
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588 INTERNAL MODIFICATIONS
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589
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590 * Support and tests for new features.
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591
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592
0
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593 CHANGES IN VERSION 0.98.1
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594 =========================
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595
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596 NEW FEATURES
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597
3
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598 First release - Wrap the w4mclassfilter R package that implements filtering of W4M data matrix, variable metadata, and sample metadata by class of sample.
0
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599
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600 *dataMatrix* *is* modified by the tool, so it *does* appear as an output file
3
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601 *sampleMetadata* *is* modified by the tool, so it *does* appear as an output file
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602 *variableMetadata* *is* modified by the tool, so it *does* appear as an output file
0
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603
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604 INTERNAL MODIFICATIONS
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605
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606 none
3
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607
5
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608 ]]></help>
0
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609 <citations>
5
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610 <!-- Giacomoni_2014 W4M 2.5 -->
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611 <citation type="doi">10.1093/bioinformatics/btu813</citation>
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612 <!-- Guitton_2017 W4M 3.0 -->
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613 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
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614 <!-- Smith_2006 XCMS -->
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615 <citation type="doi">10.1021/ac051437y</citation>
5
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616 <!-- Th_venot_2015 Urinary metabolome statistics -->
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617 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
0
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618 </citations>
3
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619 <!--
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620 vim:noet:sw=4:ts=4
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621 --> </tool>