Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 16:aae9fa9a7d4d draft default tip

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"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca-dirty"
author eschen42
date Thu, 11 Mar 2021 21:12:46 +0000
parents f9cb2244fd01
children
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rev   line source
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f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.19">
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2 <description>Filter W4M data by values or metadata</description>
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3 <requirements>
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4 <requirement type="package" version="4.0.3">r-base</requirement>
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5 <requirement type="package" version="1.1_5">r-batch</requirement>
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6 <requirement type="package" version="0.98.19">w4mclassfilter</requirement>
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7 </requirements>
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8 <command detect_errors="aggressive"><![CDATA[
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9 unset R_HOME;
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10 if [ '$centering' == 'medoid' -a '$imputation' == 'none' ]; then
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11 (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2);
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12 [ ! 1 ];
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13 else
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14 Rscript
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15 $__tool_directory__/w4mclassfilter_wrapper.R
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16 dataMatrix_in '$dataMatrix_in'
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17 sampleMetadata_in '$sampleMetadata_in'
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18 variableMetadata_in '$variableMetadata_in'
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19 sampleclassNames '$sampleclassNames'
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20 inclusive '$inclusive'
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21 wildcards '$wildcards'
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22 classnameColumn '$classnameColumn'
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23 samplenameColumn 'sampleMetadata'
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24 variable_range_filter '$variableRangeFilter'
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25 transformation '$transformation'
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26 imputation '$imputation'
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27 dataMatrix_out '$dataMatrix_out'
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28 sampleMetadata_out '$sampleMetadata_out'
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29 variableMetadata_out '$variableMetadata_out'
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30 order_vrbl '$order_vrbl'
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31 order_smpl '$order_smpl'
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32 centering '$centering';
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33 fi
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34 ]]></command>
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35 <inputs>
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36 <param name="dataMatrix_in" format="tabular" label="Data matrix" type="data"
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37 help="Choose data-matrix file (tab-separated values with sample names in first row and feature names in first column)." />
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38 <param name="sampleMetadata_in" format="tabular" label="Sample metadata" type="data"
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39 help="Choose sample-metadata file (tab-separated values with one row per sample, sample name in first column)." />
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40 <param name="variableMetadata_in" format="tabular" label="Variable metadata" type="data"
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41 help="Choose variable-metadata file (tab-separated values with one row per feature, feature name in first column)." />
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42 <param name="classnameColumn" label="Column containing the sample-class names (or treatment names)" type="text" value = "class"
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43 help="Name the column in 'Sample metadata' that has the values to be referenced by 'Sample-class names' and 'Compute centers for classes'. [default: 'class']">
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44 <sanitizer>
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45 <valid initial="string.letters">
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46 <add preset="string.digits"/>
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47 <add value="&#46;" /> <!-- dot, period -->
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48 <add value="&#95;" /> <!-- underscore -->
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49 </valid>
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50 </sanitizer>
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51 </param>
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52 <param name="sampleclassNames" label="Sample-class names (or patterns)" type="text" value = ""
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53 help="List of names (or patterns to match names) of sample classes to include or exclude. List should be comma-separated with no stray space characters. (Leave this empty to match no names.) [default: empty]">
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54 <sanitizer>
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55 <valid initial="string.letters">
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56 <add preset="string.digits"/>
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57 <add value="&#123;" /> <!-- l-curb, left-curly-bracket -->
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58 <add value="&#124;" /> <!-- pipe -->
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59 <add value="&#125;" /> <!-- r-curb, right-curly-bracket -->
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60 <add value="&#36;" /> <!-- dollar, dollar-sign -->
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61 <add value="&#40;" /> <!-- left-paren -->
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62 <add value="&#41;" /> <!-- right-paren -->
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63 <add value="&#42;" /> <!-- splat, asterisk -->
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64 <add value="&#43;" /> <!-- plus -->
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65 <add value="&#45;" /> <!-- dash, hyphen -->
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66 <add value="&#44;" /> <!-- comma -->
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67 <add value="&#46;" /> <!-- dot, period -->
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68 <add value="&#58;" /> <!-- colon -->
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69 <add value="&#59;" /> <!-- semi, semicolon -->
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70 <add value="&#63;" /> <!-- what, question mark -->
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71 <add value="&#91;" /> <!-- l-squib, left-square-bracket -->
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72 <add value="&#92;" /> <!-- whack, backslash -->
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73 <add value="&#93;" /> <!-- r-squib, right-square-bracket -->
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74 <add value="&#94;" /> <!-- hat, caret -->
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75 <add value="&#95;" /> <!-- underscore -->
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76 </valid>
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77 </sanitizer>
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78 </param>
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79 <param name="inclusive" label="Exclude/include named (or matched) sample classes" type="select" help="Indicate meaning of preceding list: either to identify classes to exclude from output or to identify classes to include in output. [default: 'filter-out']">
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80 <option value="TRUE">filter-in: &#160;&#160; Include only the named sample classes.</option>
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81 <option value="FALSE" selected="true">filter-out: &#160;&#160; Exclude only the named sample classes.</option>
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82 </param>
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83 <param name="wildcards" label="Use 'wild card patterns' or 'regular expression patterns' to match sample-class names" type="select"
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84 help="See '&lt;i&gt;Wild-card patterns to match class names&lt;/i&gt;' and '&lt;i&gt;Regular-expression patterns to match sample-class names&lt;/i&gt;' sections below. [default: 'wild-card patterns']">
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85 <option value="TRUE" selected="true">wild-card patterns: &#160;&#160; Use '*' and '?' to match sample-class names.</option>
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86 <option value="FALSE">regular-expression patterns: &#160;&#160; Use regular expressions to match sample-class names.</option>
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87 </param>
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88 <param name="variableRangeFilter" label="Variable-range filters" type="text" value = ""
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89 help="List of filters, each specifying the range of permitted values in a column of 'Variable metadata' (specified as 'column:min:max'), as described in '&lt;i&gt;Variable-range filters&lt;/i&gt;' section below. List should be comma-separated with no stray space characters. (Leave this empty for no filtering.) [default: empty]">
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90 <sanitizer>
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91 <valid initial="string.letters">
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92 <add preset="string.digits"/>
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93 <add value="&#44;" /> <!-- comma -->
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94 <add value="&#46;" /> <!-- dot, period -->
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95 <add value="&#58;" /> <!-- colon -->
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96 <add value="&#95;" /> <!-- underscore -->
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97 </valid>
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98 </sanitizer>
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99 </param>
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100 <param name="transformation" label="Data transformation" type="select"
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101 help="Choose transformation. In all cases, negative intensities become missing values. See '&lt;i&gt;Data transformation and imputation&lt;/i&gt;' section below. [default: 'none']">
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102 <option value="none" selected="true">none: &#160;&#160; Do not transform data.</option>
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103 <option value="log2">log2: &#160;&#160; Perform log base 2 transformation of data.</option>
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104 <option value="log10">log10: &#160;&#160; Perform log base 10 transformation of data.</option>
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105 </param>
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106 <param name="imputation" label="Imputation of missing values" type="select"
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107 help="Choose imputation for missing values. See '&lt;i&gt;Data transformation and imputation&lt;/i&gt;' section below. [default: 'zero']">
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108 <option value="zero" selected="true">zero: &#160;&#160; Replace missing values with zero.</option>
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109 <option value="center">center: &#160;&#160; Replace missing values with feature-median.</option>
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110 <option value="none">none: &#160;&#160; Perform no imputation. Note that 'compute centers' cannot be set to 'medoid'.</option>
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111 </param>
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112 <param name="order_smpl" label="Columns that specify order for samples" type="text" value = "sampleMetadata"
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113 help="List of sample-metadata column names for sorting samples. List should be comma-separated with no stray space characters. (This is ignored when 'Compute centers for classes' is set to either 'centroid' or 'median'.) [default: 'sampleMetadata']">
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114 <sanitizer>
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115 <valid initial="string.letters">
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116 <add preset="string.digits"/>
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117 <add value="&#46;" /> <!-- dot, period -->
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118 <add value="&#95;" /> <!-- underscore -->
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119 <add value="&#44;" /> <!-- comma -->
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120 </valid>
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121 </sanitizer>
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122 </param>
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123 <param name="order_vrbl" label="Columns that specify order for features" type="text" value = "variableMetadata"
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124 help="List of feature-metadata column names for sorting features. List should be comma-separated with no stray space characters. [default: 'variableMetadata']">
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125 <sanitizer>
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126 <valid initial="string.letters">
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127 <add preset="string.digits"/>
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128 <add value="&#46;" /> <!-- dot, period -->
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129 <add value="&#95;" /> <!-- underscore -->
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130 <add value="&#44;" /> <!-- comma -->
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131 </valid>
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132 </sanitizer>
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133 </param>
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134 <param name="centering" label="Compute centers for classes (e.g., treatments)" type="select" help="[default: 'none']">
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135 <option value="none" selected="true">none: &#160;&#160; Do not compute centers for classes/treatments.</option>
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136 <option value="centroid">centroid: &#160;&#160; For each class, compute the mean for each feature.</option>
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137 <option value="median">median: &#160;&#160; For each class, compute the median for each feature.</option>
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138 <option value="medoid">medoid: &#160;&#160; For each class, select only the most central member. Note that 'Imputation of missing values' cannot be 'none'.</option>
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139 </param>
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140 </inputs>
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141 <outputs>
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142 <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>
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143 <data name="sampleMetadata_out" format="tabular" label="${sampleMetadata_in.name}.subset" ></data>
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144 <data name="variableMetadata_out" format="tabular" label="${variableMetadata_in.name}.subset" ></data>
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145 </outputs>
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146 <tests>
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147 <!-- test 1 -->
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148 <test>
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149 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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150 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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151 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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152 <param name="classnameColumn" value="gender"/>
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153 <param name="sampleclassNames" value="M"/>
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154 <param name="wildcards" value="FALSE"/>
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155 <param name="inclusive" value="TRUE"/>
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156 <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/>
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157 <param name="transformation" value="none"/>
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158 <output name="dataMatrix_out">
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159 <assert_contents>
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160 <has_text text="747080" />
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161 <not_has_text text="13420742" />
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162 <not_has_text text="47259" />
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163 </assert_contents>
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164 </output>
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165 <output name="sampleMetadata_out">
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166 <assert_contents>
12
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167 <has_text text="HU_017" />
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168 <has_text text="HU_034" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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169 <has_text text="HU_078" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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170 <has_text text="HU_091" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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171 <has_text text="HU_093" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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172 <has_text text="HU_099" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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173 <has_text text="HU_130" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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174 <has_text text="HU_134" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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175 <has_text text="HU_138" />
10
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176 <not_has_text text="HU_028" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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177 <not_has_text text="HU_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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178 <not_has_text text="HU_060" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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179 <not_has_text text="HU_110" />
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180 <not_has_text text="HU_149" />
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181 <not_has_text text="HU_152" />
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182 <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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183 <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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184 <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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185 <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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186 <not_has_text text="HU_208" />
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187 </assert_contents>
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188 </output>
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189 <output name="variableMetadata_out">
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190 <assert_contents>
12
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191 <has_text text="HMDB00208" />
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192 <has_text text="HMDB01032" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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193 <has_text text="HMDB01101.1" />
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194 <has_text text="HMDB13189" />
10
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195 <not_has_text text="HMDB00191" />
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196 <not_has_text text="HMDB00251" />
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197 <not_has_text text="HMDB00299" />
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198 <not_has_text text="HMDB00512" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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199 <not_has_text text="HMDB00518" />
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200 <not_has_text text="HMDB00715" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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201 <not_has_text text="HMDB00822" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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202 <not_has_text text="HMDB03193" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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203 <not_has_text text="HMDB04824" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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204 <not_has_text text="HMDB10348" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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205 <not_has_text text="HMDB59717" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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206 </assert_contents>
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207 </output>
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208 </test>
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209 <!-- test 2 -->
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210 <test>
10
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211 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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212 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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213 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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214 <!-- test that hyphens in regular expressions work -->
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215 <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/>
12
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216 <param name="inclusive" value="TRUE"/>
10
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217 <param name="wildcards" value="FALSE"/>
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218 <param name="classnameColumn" value="sampleMetadata"/>
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219 <!-- test that variableRangeFilter works with tranformation -->
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220 <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
12
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221 <param name="transformation" value="log10"/>
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222 <param name="imputation" value="zero"/>
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223 <output name="dataMatrix_out" md5="5644d2ea01d072ee1d0c40e29e9d0089">
10
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224 <assert_contents>
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225 <has_text text="5.8733671" />
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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226 </assert_contents>
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227 </output>
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228 <output name="sampleMetadata_out">
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229 <assert_contents>
12
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230 <has_text text="HU_017" />
10
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231 <has_text text="HU_028" />
12
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232 <has_text text="HU_034" />
10
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233 <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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234 <has_text text="HU_060" />
12
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235 <has_text text="HU_078" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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236 <has_text text="HU_091" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
237 <has_text text="HU_093" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
238 <has_text text="HU_099" />
10
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239 <has_text text="HU_110" />
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
240 <has_text text="HU_130" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
241 <has_text text="HU_134" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
242 <has_text text="HU_138" />
10
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diff changeset
243 <has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
244 <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
245 <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
246 <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
247 <has_text text="HU_185" />
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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248 <has_text text="HU_208" />
10
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249 <not_has_text text="HU_204" />
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250 </assert_contents>
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251 </output>
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252 <output name="variableMetadata_out">
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253 <assert_contents>
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254 <has_text text="HMDB00191" />
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255 <has_text text="HMDB00208" />
12
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256 <has_text text="HMDB01032" />
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257 <has_text text="HMDB01101.1" />
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258 <has_text text="HMDB13189" />
10
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259 <not_has_text text="HMDB00251" />
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260 <not_has_text text="HMDB00299" />
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261 <not_has_text text="HMDB00512" />
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262 <not_has_text text="HMDB00518" />
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263 <not_has_text text="HMDB00715" />
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264 <not_has_text text="HMDB00822" />
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265 <not_has_text text="HMDB03193" />
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266 <not_has_text text="HMDB04824" />
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267 <not_has_text text="HMDB10348" />
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268 <not_has_text text="HMDB59717" />
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269 </assert_contents>
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270 </output>
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271 </test>
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272 <!-- test 3 -->
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273 <test>
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274 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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275 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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276 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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277 <param name="classnameColumn" value="gender"/>
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278 <param name="sampleclassNames" value="M"/>
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279 <param name="inclusive" value="TRUE"/>
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280 <param name="transformation" value="none"/>
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281 <output name="dataMatrix_out">
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282 <assert_contents>
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283 <not_has_text text="HU_028" />
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284 <not_has_text text="HU_051" />
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285 <not_has_text text="HU_060" />
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286 <not_has_text text="HU_110" />
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287 <not_has_text text="HU_149" />
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288 <not_has_text text="HU_152" />
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289 <not_has_text text="HU_175" />
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290 <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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291 <not_has_text text="HU_185" />
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292 <not_has_text text="HU_204" />
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293 <not_has_text text="HU_208" />
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294 <has_text text="HU_017" />
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295 <has_text text="HU_034" />
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296 <has_text text="HU_078" />
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297 <has_text text="HU_091" />
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298 <has_text text="HU_093" />
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299 <has_text text="HU_099" />
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300 <has_text text="HU_130" />
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301 <has_text text="HU_134" />
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302 <has_text text="HU_138" />
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303 <has_text text="HMDB03193" />
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304 <not_has_text text="HMDB00822" />
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305 <has_text text="HMDB01101" />
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306 <has_text text="HMDB01101.1" />
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307 <has_text text="HMDB10348" />
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308 <has_text text="HMDB59717" />
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309 <has_text text="HMDB13189" />
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310 <has_text text="HMDB00299" />
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311 <has_text text="HMDB00191" />
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312 <has_text text="HMDB00518" />
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313 <has_text text="HMDB00715" />
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314 <has_text text="HMDB01032" />
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315 <has_text text="HMDB00208" />
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316 <has_text text="HMDB04824" />
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317 <has_text text="HMDB00512" />
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318 <has_text text="HMDB00251" />
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319 </assert_contents>
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320 </output>
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321 </test>
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322 <!-- test 4 -->
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323 <test>
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324 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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325 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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326 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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327 <param name="classnameColumn" value="gender"/>
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328 <param name="sampleclassNames" value="*"/>
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329 <param name="wildcards" value="TRUE"/>
12
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330 <param name="inclusive" value="TRUE"/>
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331 <param name="imputation" value="zero"/>
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332 <output name="dataMatrix_out" md5="b2eac4946d3803a07606286b50451af4">
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333 <assert_contents>
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334 <not_has_text text="NA" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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335 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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336 </output>
10
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337 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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338 <assert_contents>
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339 <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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340 <has_text text="HU_028" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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341 <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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342 <has_text text="HU_060" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
343 <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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344 <has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
345 <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
346 <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
347 <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
348 <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
349 <has_text text="HU_208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
350 <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
351 <has_text text="HU_034" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
352 <has_text text="HU_078" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
353 <has_text text="HU_091" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
354 <has_text text="HU_093" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
355 <has_text text="HU_099" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
356 <has_text text="HU_130" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
357 <has_text text="HU_134" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
358 <has_text text="HU_138" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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359 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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360 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
361 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
362 <!-- test 5 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
363 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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364 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
365 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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366 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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367 <param name="classnameColumn" value="gender"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
368 <param name="sampleclassNames" value="M"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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369 <param name="wildcards" value="FALSE"/>
12
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diff changeset
370 <param name="inclusive" value="TRUE"/>
10
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diff changeset
371 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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372 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
373 <not_has_text text="HU_028" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
374 <not_has_text text="HU_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
375 <not_has_text text="HU_060" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
376 <not_has_text text="HU_110" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
377 <not_has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
378 <not_has_text text="HU_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
379 <not_has_text text="HU_175" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
380 <not_has_text text="HU_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
381 <not_has_text text="HU_185" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
382 <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
383 <not_has_text text="HU_208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
384 <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
385 <has_text text="HU_034" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
386 <has_text text="HU_078" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
387 <has_text text="HU_091" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
388 <has_text text="HU_093" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
389 <has_text text="HU_099" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
390 <has_text text="HU_130" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
391 <has_text text="HU_134" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
392 <has_text text="HU_138" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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393 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
394 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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395 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
396 <!-- test 6 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
397 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
398 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
399 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
400 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
401 <param name="classnameColumn" value="gender"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
402 <param name="sampleclassNames" value="M"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
403 <param name="wildcards" value="FALSE"/>
12
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diff changeset
404 <param name="inclusive" value="TRUE"/>
10
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diff changeset
405 <output name="variableMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
406 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
407 <has_text text="HMDB03193" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
408 <not_has_text text="HMDB00822" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
409 <has_text text="HMDB01101" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
410 <has_text text="HMDB01101.1" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
411 <has_text text="HMDB10348" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
412 <has_text text="HMDB59717" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
413 <has_text text="HMDB13189" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
414 <has_text text="HMDB00299" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
415 <has_text text="HMDB00191" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
416 <has_text text="HMDB00518" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
417 <has_text text="HMDB00715" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
418 <has_text text="HMDB01032" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
419 <has_text text="HMDB00208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
420 <has_text text="HMDB04824" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
421 <has_text text="HMDB00512" />
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diff changeset
422 <has_text text="HMDB00251" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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423 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
424 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
425 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
426 <!-- test 7 -->
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diff changeset
427 <test>
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diff changeset
428 <param name="dataMatrix_in" value="input_nofilter_dataMatrix.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
429 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
430 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
431 <param name="classnameColumn" value="gender"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
432 <param name="sampleclassNames" value="M"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
433 <param name="wildcards" value="FALSE"/>
12
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diff changeset
434 <param name="inclusive" value="TRUE"/>
10
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diff changeset
435 <output name="variableMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
436 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
437 <has_text text="HMDB03193" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
438 <not_has_text text="HMDB00822" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
439 <has_text text="HMDB01101" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
440 <has_text text="HMDB01101.1" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
441 <has_text text="HMDB10348" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
442 <has_text text="HMDB59717" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
443 <not_has_text text="HMDB13189" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
444 <has_text text="HMDB00299" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
445 <has_text text="HMDB00191" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
446 <has_text text="HMDB00518" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
447 <has_text text="HMDB00715" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
448 <has_text text="HMDB01032" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
449 <has_text text="HMDB00208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
450 <has_text text="HMDB04824" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
451 <has_text text="HMDB00512" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
452 <has_text text="HMDB00251" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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453 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
454 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
455 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
456 <!-- test 8 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
457 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
458 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
459 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
460 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
461 <param name="classnameColumn" value="gender"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
462 <param name="sampleclassNames" value="[Mm],[fF]"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
463 <param name="wildcards" value="FALSE"/>
12
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diff changeset
464 <param name="inclusive" value="TRUE"/>
10
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diff changeset
465 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
466 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
467 <has_text text="HU_028" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
468 <has_text text="HU_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
469 <has_text text="HU_060" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
470 <has_text text="HU_110" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
471 <has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
472 <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
473 <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
474 <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
475 <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
476 <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
477 <has_text text="HU_208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
478 <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
479 <has_text text="HU_034" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
480 <has_text text="HU_078" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
481 <has_text text="HU_091" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
482 <has_text text="HU_093" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
483 <has_text text="HU_099" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
484 <has_text text="HU_130" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
485 <has_text text="HU_134" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
486 <has_text text="HU_138" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
487 </assert_contents>
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diff changeset
488 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
489 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
490 <!-- test 9 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
491 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
492 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
493 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
494 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
495 <param name="classnameColumn" value=""/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
496 <param name="sampleclassNames" value="M"/>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
497 <param name="wildcards" value="FALSE"/>
12
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diff changeset
498 <param name="inclusive" value="TRUE"/>
10
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diff changeset
499 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
500 <assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
501 <has_text text="HU_028" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
502 <has_text text="HU_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
503 <has_text text="HU_060" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
504 <has_text text="HU_110" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
505 <has_text text="HU_149" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
506 <has_text text="HU_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
507 <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
508 <has_text text="HU_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
509 <has_text text="HU_185" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
510 <not_has_text text="HU_204" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
511 <has_text text="HU_208" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
512 <has_text text="HU_017" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
513 <has_text text="HU_034" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
514 <has_text text="HU_078" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
515 <has_text text="HU_091" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
516 <has_text text="HU_093" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
517 <has_text text="HU_099" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
518 <has_text text="HU_130" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
519 <has_text text="HU_134" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
520 <has_text text="HU_138" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
521 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
522 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
523 </test>
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
524 <!-- test 10 - extends test4 with no imputation rather than zero imputation -->
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
525 <test>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
526 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
527 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
528 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
529 <param name="classnameColumn" value="gender"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
530 <param name="sampleclassNames" value="*"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
531 <param name="wildcards" value="TRUE"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
532 <param name="inclusive" value="TRUE"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
533 <param name="imputation" value="none"/>
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
534 <output name="dataMatrix_out" md5="6200dfa77d09c56e434f80b1a23b3393">
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
535 <assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
536 <not_has_text text="HU_204" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
537 <has_text text="NA" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
538 <has_text text="HU_028" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
539 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
540 </output>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
541 <output name="sampleMetadata_out">
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
542 <assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
543 <not_has_text text="HU_204" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
544 <has_text text="HU_028" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
545 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
546 </output>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
547 </test>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
548 <!-- test 11 - extends test4 with center imputation rather than zero imputation -->
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
549 <test>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
550 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
551 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
552 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
553 <param name="classnameColumn" value="gender"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
554 <param name="sampleclassNames" value="*"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
555 <param name="wildcards" value="TRUE"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
556 <param name="inclusive" value="TRUE"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
557 <param name="imputation" value="center"/>
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
558 <output name="dataMatrix_out" md5="a404278c5c9ffd5bdadf346c4f8a0184">
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
559 <assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
560 <not_has_text text="HU_204" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
561 <not_has_text text="NA" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
562 <has_text text="HU_028" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
563 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
564 </output>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
565 <output name="sampleMetadata_out">
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
566 <assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
567 <not_has_text text="HU_204" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
568 <has_text text="HU_028" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
569 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
570 </output>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
571 </test>
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
572 <!-- test 12 - select medoid for class -->
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
573 <test>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
574 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
575 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
576 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
577 <param name="classnameColumn" value="gender"/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
578 <param name="sampleclassNames" value=""/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
579 <param name="wildcards" value="TRUE"/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
580 <param name="inclusive" value="FALSE"/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
581 <param name="imputation" value="zero"/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
582 <param name="order_vrbl" value="rt"/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
583 <param name="order_smpl" value="gender"/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
584 <param name="centering" value="medoid"/>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
585 <output name="dataMatrix_out" md5="c91bbfbf30004fa24b05a67ec479bfb1">
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
586 <assert_contents>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
587 <not_has_text text="1013302" />
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
588 <has_text text="4763576" />
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
589 <has_text text="2003278" />
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
590 <has_text text="26222916" />
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
591 </assert_contents>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
592 </output>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
593 <output name="sampleMetadata_out">
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
594 <assert_contents>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
595 <not_has_text text="HU_099" />
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
596 <not_has_text text="HU_185" />
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
597 <has_text text="HU_110" />
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
598 <has_text text="HU_078" />
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
599 </assert_contents>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
600 </output>
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diff changeset
601 </test>
15
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diff changeset
602 <!-- test 13 -->
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diff changeset
603 <test>
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604 <param name="dataMatrix_in" value="input_med1_dm.tsv"/>
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605 <param name="sampleMetadata_in" value="input_med1_sm.tsv"/>
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606 <param name="variableMetadata_in" value="input_med1_vm.tsv"/>
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diff changeset
607 <param name="classnameColumn" value="pcgroup"/>
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608 <param name="sampleclassNames" value=""/>
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609 <param name="wildcards" value="TRUE"/>
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610 <param name="inclusive" value="FALSE"/>
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611 <param name="imputation" value="zero"/>
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612 <param name="order_vrbl" value="sample"/>
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613 <param name="order_smpl" value="pcgroup"/>
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614 <param name="centering" value="medoid"/>
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615 <output name="sampleMetadata_out">
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diff changeset
616 <assert_contents>
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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diff changeset
617 <has_text text="X10" />
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diff changeset
618 <has_text text="M70T1043" />
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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diff changeset
619 <has_text text="70.01229" />
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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620 <has_text text="1042.837" />
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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diff changeset
621 <has_text text="X345" />
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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diff changeset
622 <has_text text="M74T33" />
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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diff changeset
623 <not_has_text text="M70T1042_1" />
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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624 <not_has_text text="M74T34" />
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625 </assert_contents>
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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diff changeset
626 </output>
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diff changeset
627 <output name="dataMatrix_out">
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628 <assert_contents>
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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diff changeset
629 <has_text text="X10" />
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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diff changeset
630 <has_text text="X345" />
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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631 </assert_contents>
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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632 </output>
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633 </test>
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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634 </tests>
15
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635 <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation:
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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636 https://web.archive.org/web/20161014025757/http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/
f9cb2244fd01 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit aaac8e2f8de03c01e5064abf8a2e30020fabe7ca"
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637 -->
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
638 <help><![CDATA[
0
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639
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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640
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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641 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
0
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642
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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643 --------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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644
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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645
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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646 **R package**
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647
14
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648 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).
0
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649
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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650 -----------------------------------------------------------------------------------------------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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651
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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652
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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653 **Tool updates**
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654
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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655 See https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper#news
0
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656
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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657 ---------------------------------------------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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658
14
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659 ======================================================
15
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660 "W4M Data Subset" - Filter Workflow4Metabolomics data
14
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661 ======================================================
8
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662
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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663 ----------
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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664 Motivation
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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665 ----------
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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666
14
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667 LC-MS metabolomics experiments seek to resolve "features", i.e., species that have distinct chromatographic retention time ("rt") and (after ionization) mass-to-charge ratio ("*m/z*" or "mz").
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diff changeset
668 (If a chemical is fragmented or may have a variety of adducts, several features will result.)
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669 Data for a sample are collected as mass-spectral intensities, each of which is associated with a position on a 2D plane with dimensions of rt and *m/z*.
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670 Ideally, features would be sufficiently reproducible among sample-runs to distinguish features that are similar among samples from those that differ.
8
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671
14
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672 For liquid chromatography, the retention time for a species can vary considerably from one chromatography run to the next.
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673 The Workflow4Metabolomics suite of Galaxy tools (W4M, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017])
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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674 uses the XCMS preprocessing tools [Smith *et al.*, 2006]
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diff changeset
675 for "retention-time correction" to align features among samples.
8
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676 Features may be better aligned if pooled samples and blanks are included.
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677
14
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diff changeset
678 Multivariate statistical tools may be used to discover clusters of similar samples [Th]]>&#233;<![CDATA[venot *et al.*, 2015].
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679 However, once retention-time alignment of features has been achieved among samples in LC-MS datasets:
8
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680
14
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diff changeset
681 - The presence of pools and blanks may confound identification and separation of sample clusters.
8
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682 - Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance.
0
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683
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684 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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685 Description
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686 -----------
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687
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688 The **W4M Data Subset** tool **selects subsets of samples, features, or data values** and **conditions the data** for further analysis.
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689
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690 - The tool takes as input the *dataMatrix*, *sampleMetadata*, and *variableMetadata* datasets produced by W4M's XCMS and CAMERA [Kuhl *et al.*, 2012] tools.
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691 - The tool produces the same trio of output datasets, modified as described below.
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692
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693 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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694
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695 - *Sample filtering:* Samples may be selected by designating a "sample class" column in *sampleMetadata* and specifying criteria to include or exclude samples based on the contents of this column.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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696 - *Feature filtering:* Features may be selected by specifying minimum or maximum value (or both) allowable in columns of *variableMetadata*.
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697 - *Intensity filtering:* To exclude minimal features from consideration, a lower bound may be specified for the maximum intensity for a feature across all samples (i.e., for a row in *dataMatrix*).
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698
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699 This tool also conditions data for statistical analysis:
8
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700
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701 - Samples that are missing from either *sampleMetadata* or *dataMatrix* are eliminated.
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702 - Features that are missing from either *variableMetadata* or *dataMatrix* are eliminated.
8
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703 - Features and samples that have zero variance are eliminated.
14
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704 - Samples and features are ordered consistently in *variableMetadata*, *sampleMetadata*, and *dataMatrix*.
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705 (The columns for sorting *variableMetadata* or *sampleMetadata* may be specified.)
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706 - The names of the first columns of *variableMetadata* and *sampleMetadata* are set respectively to "variableMetadata" and "sampleMetadata".
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707 - If desired, the values in *dataMatrix* may be log-transformed.
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708 - Negative intensities become missing values (before missing-value replacement is performed).
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709 - If desired, each missing value in *dataMatrix* may be replaced with zero or the median value observed for the corresponding feature.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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710 - If desired, a "center" for each treatment can be computed in lieu of the samples for that treatment.
8
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711
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712 This tool may be applied several times sequentially, which may be useful for:
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713
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714 - analyzing subsets of samples for progressively smaller sets of treatment levels, or
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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715 - choosing subsets of samples or features, respectively based on criteria in columns of *sampleMetadata* or *variableMetadata*.
3
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716
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717 -----------------
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718 Workflow Position
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719 -----------------
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720
8
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721 This tool can be used at any point downstream of Preprocessing.
0
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722
8
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723 - Possible upstream tool categories: Preprocessing, Quality Control, Statistical Analysis, Filter and Sort
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724 - Possible downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
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725
0
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726 -----------
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727 Input files
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728 -----------
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729
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730 +------------------------+---------------------------------------+------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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731 | File | Contents | Format |
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732 +========================+=======================================+============+
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733 | Data matrix | per-feature, per-sample intensities | tabular |
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734 +------------------------+---------------------------------------+------------+
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735 | Sample metadata | metadata for samples | tabular |
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736 +------------------------+---------------------------------------+------------+
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737 | Variable metadata | metadata for features | tabular |
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738 +------------------------+---------------------------------------+------------+
0
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739
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diff changeset
740
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741 ----------
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742 Parameters
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743 ----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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744
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745 Data matrix
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746 | feature x sample **dataMatrix** (tab-separated values) file of the numeric data matrix, with period-character ('.') as decimal, and 'NA' for missing values.
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747 | The file must not contain metadata apart from the required row and column names.
0
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748 |
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749
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750 Sample metadata
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751 | sample x metadata **sampleMetadata** (tab-separated values) file of the numeric and/or character sample metadata, with period-character ('.') as decimal, and 'NA' for missing values.
0
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752 |
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753
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754 Variable metadata
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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755 | variable x metadata **variableMetadata** (tab-separated values) file of the numeric and/or character variable metadata, with period-character ('.') as decimal, and 'NA' for missing values.
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756 |
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757
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758 Column containing the sample-class names (default = '``class``')
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759 | name of the column in **sampleMetadata** that has the values to be tested against the '``Sample-class names``' input parameter or to be referenced by the '``Compute centers for classes``' input parameter.
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760 | Only letters, digits, periods, and underscores are permitted.
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761 |
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762
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763 Sample-class names (default = no names)
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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764 | names (or regular expressions to match names) of sample-classes to include or exclude
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765 | (Separate names with commas, without any extra space characters.)
0
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766 |
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767
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768 Exclude/include named (or matched) classes (default = '``filter-out``')
8
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769 | '``filter-in``' - include only the named sample-classes
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770 | '``filter-out``' - exclude only the named sample-classes
0
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771 |
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772
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773 Use 'wild card patterns' or 'regular expression patterns' (default = '``wild-card patterns``')
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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774 | '``wild-card patterns``' - use wild cards to match names of sample-classes (see the *'Wild-card patterns to match class names'* section below.)
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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775 | '``regular-expression patterns``' - use regular expressions to match the named sample-classes (see the *'Regular-expression patterns to match class names'* section below.)
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776 |
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diff changeset
777
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
778 Variable-range filters (default = no filters)
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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779 | variable-range filters (see the *'Variable-range filters'* section below)
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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780 | (Separate filter expressions with commas, without any extra space characters.)
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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781 |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
782
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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783 Data transformation (default = '``none``')
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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784 | '``none``' - Do not transform data matrix values.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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785 | '``log2``' - Take the log base 2 of the values in the data matrix.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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786 | '``log10``' - Take the log base 10 of the values in the data matrix.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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787 |
14
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788 | Note that negative intensities become missing values regardless of the choice made here.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
789 |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
790
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
791 Imputation of missing values (default = '``zero``')
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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792 | '``none``' - Do not impute data matrix values.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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793 | '``zero``' - Negative and missing values are imputed to zero.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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794 | '``center``' - For each feature, negative and missing values are imputed to the median of other values.
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
795 |
14
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diff changeset
796 | Note well: For '``none``' option, '``Compute centers for classes``' cannot be set to '``medoid``'.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
797 |
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
798
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
799 Columns that specify order for samples (default = '``sampleMetadata``')
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
800 | names of the columns in **sampleMetadata** that is used to sort samples; only letters, digits, periods, and underscores are permitted.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
801 | (Separate column names with commas, without any extra space characters.)
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
802 |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
803
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
804 Columns that specify order for features (default = '``variableMetadata``')
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
805 | names of the columns in **variableMetadata** that is used to sort features; only letters, digits, periods, and underscores are permitted.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
806 | (Separate column names with commas, without any extra space characters.)
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
807 |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
808
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
809 Compute centers for classes, e.g., treatments (default = '``none``')
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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810 | '``none``' - Return all samples; do not compute centers for classes/treatments.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
811 | '``centroid``' - For each treatment, return only the centroid (the treatment-center computed as the mean intensity for each feature).
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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812 | '``median``' - For each treatment, return only the treatment-center computed as the median intensity for each feature.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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813 | '``medoid``' - For each treatment, return only the medoid (the sample most similar to the other samples for that treatment).
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
814 |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
815 | Note well: For '``medoid``' option, '``Imputation of missing values``' cannot be set to '``none``'.
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
816 |
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
817
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
818 ------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
819 Output files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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820 ------------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
821
2
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diff changeset
822 sampleMetadata
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
823 | (tab-separated values) file.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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824 | If centering is '``none``' or '``medoid``', this will be 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)
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
825 | If centering is '``centroid``' or '``median``', most columns will be replaced with the treatment name and the number of samples for that treatment.
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
826 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
827
2
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diff changeset
828 variableMetadata
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
829 | (tab-separated values) file identical to the **variableMetadata** file given as an input argument, excepting lacking rows for variables (LC-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)
2
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diff changeset
830 |
23c6d271def9 planemo upload
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diff changeset
831
23c6d271def9 planemo upload
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diff changeset
832 dataMatrix
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
833 | (tab-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
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
834 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
835
2
23c6d271def9 planemo upload
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diff changeset
836
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
837 -----------------------------------------
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
838 Wild-card patterns to match class names
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
839 -----------------------------------------
4
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diff changeset
840
14
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parents: 13
diff changeset
841 W4M Data Subset supports use of "wild card" patterns to select class-names.
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
842
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
843 - use '``?``' to match a single character
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
844 - use '``*``' to match zero or more characters
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
845 - the entire pattern must match the sample name
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
846
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
847 For example
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
848
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
849 - '``??.samp*``' matches '``my.sample``' but not '``my.own.sample``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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850 - '``*.sample``' matches '``my.sample``' and '``my.own.sample``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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851 - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``'
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diff changeset
852
8
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853 --------------------------------------------------
14
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diff changeset
854 Regular-expression patterns to match class names
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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855 --------------------------------------------------
4
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diff changeset
856
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
857 W4M Data Subset supports use of R "extended regular expression" patterns to select class-names.
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
858
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
859 R extended regular expressions, which allow precise pattern-matching and are exhaustively defined at
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
860 https://stat.ethz.ch/R-manual/R-devel/library/base/html/regex.html
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
861
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
862 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
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diff changeset
863
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diff changeset
864 - '``^``' matches the beginning of a class-name
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
865 - '``$``' matches the end of a class-name
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866 - '``.``' outside of square brackets matches a single character
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
867 - '``*``' matches character specified immediately before zero or more times
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
868 - square brackets specify a set of characters to be matched.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
eschen42
parents: 3
diff changeset
869
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
870 Within square brackets
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
871
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
eschen42
parents: 3
diff changeset
872 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
eschen42
parents: 3
diff changeset
873 - '``-``' is used to specify ranges of characters
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
874
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
eschen42
parents: 3
diff changeset
875 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**
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
876
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
877 First Example: Consider a field of class-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
878
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
879 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
eschen42
parents: 3
diff changeset
880 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
eschen42
parents: 3
diff changeset
881 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
eschen42
parents: 3
diff changeset
882 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-classes as '``front3,front6,front9,marq3,marq6,marq9``'
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
eschen42
parents: 3
diff changeset
883
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
884 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
885
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
886 - '``^[A-Z][A-Z][0-9][0-9]*$``' MATCHES '``**^AB0123$**``'
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
887 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' MATCHES '``**^AB0123$**``'
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
888 - '``^[A-Z][0-9]*``' MATCHES '``**^A** B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
889 - '``^[A-Z][A-Z][0-9]``' MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
890 - '``^[A-Z][A-Z]*[0-9][0-9]$``' DOES NOT MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
891 - '``^[A-Z][0-9]*$``' DOES NOT MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
892
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
893 ----------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
894 Variable-range filters
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
895 ----------------------
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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parents: 3
diff changeset
896
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
897 An array of range-specification strings may be supplied in the '``Variable-range filters``'
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
898 argument. If supplied, only features having numerical values in the specified column
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
899 of **variableMetadata** that fall within the specified ranges will be retained
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
900 in the output. Each range is a string of three colon-separated values (e.g., '``mz:200:800``') in the
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
901 following order:
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
902
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
903 - the **name of a column** of **variableMetadata** which must have numerical data (only letters, digits, periods, and underscores are permitted in the name itself), e.g., '``mz``';
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
904 - the **minimum allowed value** in that column for the feature to be retained, e.g., '``200``';
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
905 - the **maximum allowed value**, e.g., '``800``'.
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
906
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
907 Note for the range specification strings:
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
908
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
909 - **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)
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
910 - **If the name supplied in the first field** is '``FEATMAX``', then the string is defining the **threshold for the maximum intensity** for each feature in the dataMatrix.
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
911
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
912 - For example, '``FEATMAX:1e6:``' would specify that any feature would be excluded if no sample had an intensity for that feature greater than 1,000,000.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
913 - Although a maximum may be specified, it seems unlikely that this would be useful. Note that when the "maximum" is less than the "minimum" for the FEATMAX range specification, then the specification is ignored.
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
914
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
915 ----------------------------------
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
916 Data transformation and imputation
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
917 ----------------------------------
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
918
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
919 Data may optionally be log2- or log10-transformed.
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
920
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
921 Negative intensities are always substituted with missing values before imputation, even when no transformation is chosen.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
922
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
923 Missing intensity data values may optionally be imputed. Missing values may be substituted:
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
924
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
925 - with zeros (as may be appropriate for univariate analysis)
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
926 - with the median for the feature (as may be appropriate for multivariate analysis).
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
927
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
928 - Note that the median feature-intensity is computed for the samples *before* variable-range filters are applied.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
929
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
930 -----------------------------------------
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
931 Optional Computation of Treatment Centers
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
932 -----------------------------------------
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
933
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
934 A "center" for each treatment may be computed in lieu of all the samples for each treatment.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
935
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
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936 - '``none``' - Return all samples; do not compute centers.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
937 - '``centroid``' - For each treatment, return only the centroid (the treatment-center computed as the mean intensity for each feature).
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
938 - '``median``' - For each treatment, return only the treatment-center computed as the median intensity for each feature.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
939 - '``medoid``' - For each treatment, return only the medoid (the sample most similar to the other samples for that treatment). This choice requires that the '``Imputation of missing values``' argument must not be set to '``none``'.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
940
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
941 The medoid is the sample having the smallest sum of its distances from other samples in the treatment:
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
942
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
943 - Because principal components are uncorrelated, distances are computed in the space defined by the principal-component scores to minimize the distortion of computed distances by correlated features.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
944 - Because principal components are used to compute distances, no missing values are permitted, which is why the '``Imputation of missing values``' argument must not be set to '``none``'.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
945 - The distances are used to identify the medoid using code adapted from https://web.archive.org/web/20191231012914/https://www.biostars.org/p/11987/#11989
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
946
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
947 -----------------------------------------------------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
948
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
949 ----------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
950 WORKING EXAMPLES
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
951 ----------------
2
23c6d271def9 planemo upload
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diff changeset
952
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
953 -----------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
954 Input Files
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
955 -----------
2
23c6d271def9 planemo upload
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parents: 0
diff changeset
956
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
957 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
958 | 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
959 +======================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
960 | 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
961 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
962 | 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
963 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
964 | 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
965 +------------------------------------------------------------------------------------------------------------------------------------------------------+
2
23c6d271def9 planemo upload
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diff changeset
966
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
967 -------------------------------
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
968 Example without Range-Filtering
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
969 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
970
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
971 This example retains only samples whose '``gender``' attribute is '``M``'.
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
972
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
973 **Input parameters**
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
974
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
975 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
976 | Input Parameter | Value |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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977 +=============================================+===============================+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
978 | Column that names the sample class | gender |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
979 +---------------------------------------------+-------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
980 | Sample-class names | M |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
981 +---------------------------------------------+-------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
982 | Exclude/include named classes | filter-in |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
983 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
984 | Use 'wild-cards' or 'regular expressions' | wild-cards |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
985 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
986 | Variable range-filters | (Leave this field empty.) |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
987 +---------------------------------------------+-------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
988 | Data transformation | none |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
989 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
990 | Missing-value imputation | center |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
991 +---------------------------------------------+-------------------------------+
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
eschen42
parents: 12
diff changeset
992 | Sample-sort column | sampleMetadata |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
993 +---------------------------------------------+-------------------------------+
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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parents: 12
diff changeset
994 | Feature-sort column | variableMetadata |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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parents: 12
diff changeset
995 +---------------------------------------------+-------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
996 | Compute centers for classes | none |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
997 +---------------------------------------------+-------------------------------+
2
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diff changeset
998
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
999 **Expected outputs**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
1000
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
1001 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
1002 | 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
1003 +===================+=================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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parents: 9
diff changeset
1004 | 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
1005 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
1006 | 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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parents: 9
diff changeset
1007 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
1008 | 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
1009 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
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
1010
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
1011 ----------------------------
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
1012 Example with Range-Filtering
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
1013 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
1014
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
1015 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.
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
1016 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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diff changeset
1017
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
1018 **Input parameters**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
1019
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
1020 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
1021 | Input Parameter | Value |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
1022 +=============================================+===================================+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
1023 | Column that names the sample class | sampleMetadata |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
1024 +---------------------------------------------+-----------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1025 | Sample-class names | HU_13[48] |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
1026 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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parents: 13
diff changeset
1027 | Exclude/include named classes | filter-out |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
1028 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
1029 | Use 'wild-cards' or 'regular expressions' | regular-expressions |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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parents: 11
diff changeset
1030 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
1031 | Variable range-filters | FEATMAX:20.93157:,mz:200:,rt::800 |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
1032 +---------------------------------------------+-----------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
1033 | Data transformation | log2 |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
1034 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
1035 | Missing-value imputation | zero |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
1036 +---------------------------------------------+-----------------------------------+
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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parents: 12
diff changeset
1037 | Sample-sort column | sampleMetadata |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
eschen42
parents: 12
diff changeset
1038 +---------------------------------------------+-----------------------------------+
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
eschen42
parents: 12
diff changeset
1039 | Feature-sort column | variableMetadata |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
eschen42
parents: 12
diff changeset
1040 +---------------------------------------------+-----------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1041 | Compute centers for classes | none |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1042 +---------------------------------------------+-----------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
1043
2
23c6d271def9 planemo upload
eschen42
parents: 0
diff changeset
1044 **Expected outputs**
23c6d271def9 planemo upload
eschen42
parents: 0
diff changeset
1045
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1046 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1047 | Expected Output | Download from URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1048 +===================+===================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1049 | 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
1050 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1051 | 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
1052 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1053 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/rangefilter_variableMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1054 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1055
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1056 --------------------------------
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1057 Example with Treatment-Centering
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1058 --------------------------------
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1059
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1060 This example retains only the samples that are medoids for their gender.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1061
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1062 **Input parameters**
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1063
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1064 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1065 | Input Parameter | Value |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1066 +=============================================+===================================+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1067 | Column that names the sample class | gender |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1068 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1069 | Sample-class names | (Leave this field empty.) |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1070 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1071 | Exclude/include named classes | filter-out |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1072 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1073 | Use 'wild-cards' or 'regular expressions' | wild-cards |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1074 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1075 | Variable range-filters | (Leave this field empty.) |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1076 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1077 | Data transformation | none |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1078 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1079 | Missing-value imputation | zero |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1080 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1081 | Sample-sort column | gender |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1082 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1083 | Feature-sort column | rt |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1084 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1085 | Compute centers for classes | medoid |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1086 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1087
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1088 **Expected outputs**
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1089
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1090 +-------------------+----------------------------------------------------------------------------------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1091 | Expected Output | Download from URL |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1092 +===================+==========================================================================================================+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1093 | Data matrix | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_dm.tsv |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1094 +-------------------+----------------------------------------------------------------------------------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1095 | Sample metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_sm.tsv |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1096 +-------------------+----------------------------------------------------------------------------------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1097 | Variable metadata | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter/master/tests/testthat/exp_cent_medoid_vm.tsv |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1098 +-------------------+----------------------------------------------------------------------------------------------------------+
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1099 ]]></help>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1100 <citations>
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1101 <!-- Giacomoni_2014 W4M 2.5 -->
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1102 <citation type="doi">10.1093/bioinformatics/btu813</citation>
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1103 <!-- Guitton_2017 W4M 3.0 -->
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1104 <citation type="doi">10.1016/j.biocel.2017.07.002</citation>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1105 <!-- Kuhl_2012 CAMERA -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1106 <citation type="doi">10.1021/ac202450g</citation>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1107 <!-- Smith_2006 XCMS -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1108 <citation type="doi">10.1021/ac051437y</citation>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1109 <!-- Thevenot_2015 Urinary metabolome statistics -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1110 <citation type="doi">10.1021/acs.jproteome.5b00354</citation>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1111 </citations>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1112 <!--
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1113 vim:noet:sw=4:ts=4
3
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
eschen42
parents: 2
diff changeset
1114 --> </tool>