Mercurial > repos > eschen42 > w4mclassfilter

annotate w4mclassfilter.xml @ 14:87ec0d3c2266 draft

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"planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
author eschen42
date Fri, 03 Jan 2020 11:07:39 -0500
parents c18040b6e8b9
children f9cb2244fd01
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14
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1 <tool id="w4mclassfilter" name="W4m Data Subset" version="0.98.18">
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2 <description>Filter W4M data by values or metadata</description>
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3 <!-- Here is the hyphenation standard that I *try* to apply consistently in my documentation:
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4 https://web.archive.org/web/20161014025757/http://www.sandranoonan.com/dont-let-hyphenation-drive-crazy/
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5 -->
10
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6 <requirements>
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7 <requirement type="package" version="3.6.2">r-base</requirement>
12
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8 <requirement type="package" version="1.1_5">r-batch</requirement>
14
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9 <requirement type="package" version="0.98.18">w4mclassfilter</requirement>
10
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10 </requirements>
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11 <command detect_errors="aggressive"><![CDATA[
12
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12 unset R_HOME;
14
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13 if [ '$centering' == 'medoid' -a '$imputation' == 'none' ]; then
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14 (echo 'medoid' centering may not be chosen with imputation 'none' 1>&2);
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15 [ ! 1 ];
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16 else
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17 Rscript
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18 $__tool_directory__/w4mclassfilter_wrapper.R
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19 dataMatrix_in '$dataMatrix_in'
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20 sampleMetadata_in '$sampleMetadata_in'
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21 variableMetadata_in '$variableMetadata_in'
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22 sampleclassNames '$sampleclassNames'
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23 inclusive '$inclusive'
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24 wildcards '$wildcards'
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25 classnameColumn '$classnameColumn'
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26 samplenameColumn 'sampleMetadata'
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27 variable_range_filter '$variableRangeFilter'
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28 transformation '$transformation'
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29 imputation '$imputation'
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30 dataMatrix_out '$dataMatrix_out'
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31 sampleMetadata_out '$sampleMetadata_out'
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32 variableMetadata_out '$variableMetadata_out'
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33 order_vrbl '$order_vrbl'
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34 order_smpl '$order_smpl'
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35 centering '$centering';
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36 fi
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37 ]]></command>
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38 <inputs>
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39 <param name="dataMatrix_in" format="tabular" label="Data matrix" type="data"
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40 help="Choose data-matrix file (tab-separated values with sample names in first row and feature names in first column)." />
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41 <param name="sampleMetadata_in" format="tabular" label="Sample metadata" type="data"
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42 help="Choose sample-metadata file (tab-separated values with one row per sample, sample name in first column)." />
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43 <param name="variableMetadata_in" format="tabular" label="Variable metadata" type="data"
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44 help="Choose variable-metadata file (tab-separated values with one row per feature, feature name in first column)." />
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45 <param name="classnameColumn" label="Column containing the sample-class names (or treatment names)" type="text" value = "class"
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46 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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47 <sanitizer>
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48 <valid initial="string.letters">
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49 <add preset="string.digits"/>
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50 <add value="&#46;" /> <!-- dot, period -->
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51 <add value="&#95;" /> <!-- underscore -->
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52 </valid>
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53 </sanitizer>
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54 </param>
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55 <param name="sampleclassNames" label="Sample-class names (or patterns)" type="text" value = ""
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56 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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57 <sanitizer>
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58 <valid initial="string.letters">
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59 <add preset="string.digits"/>
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60 <add value="&#123;" /> <!-- l-curb, left-curly-bracket -->
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61 <add value="&#124;" /> <!-- pipe -->
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62 <add value="&#125;" /> <!-- r-curb, right-curly-bracket -->
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63 <add value="&#36;" /> <!-- dollar, dollar-sign -->
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64 <add value="&#40;" /> <!-- left-paren -->
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65 <add value="&#41;" /> <!-- right-paren -->
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66 <add value="&#42;" /> <!-- splat, asterisk -->
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67 <add value="&#43;" /> <!-- plus -->
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68 <add value="&#45;" /> <!-- dash, hyphen -->
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69 <add value="&#44;" /> <!-- comma -->
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70 <add value="&#46;" /> <!-- dot, period -->
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71 <add value="&#58;" /> <!-- colon -->
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72 <add value="&#59;" /> <!-- semi, semicolon -->
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73 <add value="&#63;" /> <!-- what, question mark -->
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74 <add value="&#91;" /> <!-- l-squib, left-square-bracket -->
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75 <add value="&#92;" /> <!-- whack, backslash -->
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76 <add value="&#93;" /> <!-- r-squib, right-square-bracket -->
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77 <add value="&#94;" /> <!-- hat, caret -->
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78 <add value="&#95;" /> <!-- underscore -->
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79 </valid>
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80 </sanitizer>
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81 </param>
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82 <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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83 <option value="TRUE">filter-in: &#160;&#160; Include only the named sample classes.</option>
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84 <option value="FALSE" selected="true">filter-out: &#160;&#160; Exclude only the named sample classes.</option>
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85 </param>
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86 <param name="wildcards" label="Use 'wild card patterns' or 'regular expression patterns' to match sample-class names" type="select"
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87 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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88 <option value="TRUE" selected="true">wild-card patterns: &#160;&#160; Use '*' and '?' to match sample-class names.</option>
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89 <option value="FALSE">regular-expression patterns: &#160;&#160; Use regular expressions to match sample-class names.</option>
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90 </param>
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91 <param name="variableRangeFilter" label="Variable-range filters" type="text" value = ""
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92 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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93 <sanitizer>
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94 <valid initial="string.letters">
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95 <add preset="string.digits"/>
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96 <add value="&#44;" /> <!-- comma -->
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97 <add value="&#46;" /> <!-- dot, period -->
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98 <add value="&#58;" /> <!-- colon -->
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99 <add value="&#95;" /> <!-- underscore -->
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100 </valid>
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101 </sanitizer>
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102 </param>
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103 <param name="transformation" label="Data transformation" type="select"
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104 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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105 <option value="none" selected="true">none: &#160;&#160; Do not transform data.</option>
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106 <option value="log2">log2: &#160;&#160; Perform log base 2 transformation of data.</option>
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107 <option value="log10">log10: &#160;&#160; Perform log base 10 transformation of data.</option>
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108 </param>
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109 <param name="imputation" label="Imputation of missing values" type="select"
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110 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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111 <option value="zero" selected="true">zero: &#160;&#160; Replace missing values with zero.</option>
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112 <option value="center">center: &#160;&#160; Replace missing values with feature-median.</option>
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113 <option value="none">none: &#160;&#160; Perform no imputation. Note that 'compute centers' cannot be set to 'medoid'.</option>
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114 </param>
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115 <param name="order_smpl" label="Columns that specify order for samples" type="text" value = "sampleMetadata"
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116 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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117 <sanitizer>
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118 <valid initial="string.letters">
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119 <add preset="string.digits"/>
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120 <add value="&#46;" /> <!-- dot, period -->
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121 <add value="&#95;" /> <!-- underscore -->
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122 <add value="&#44;" /> <!-- comma -->
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123 </valid>
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124 </sanitizer>
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125 </param>
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126 <param name="order_vrbl" label="Columns that specify order for features" type="text" value = "variableMetadata"
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127 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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128 <sanitizer>
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129 <valid initial="string.letters">
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130 <add preset="string.digits"/>
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131 <add value="&#46;" /> <!-- dot, period -->
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132 <add value="&#95;" /> <!-- underscore -->
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133 <add value="&#44;" /> <!-- comma -->
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134 </valid>
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135 </sanitizer>
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136 </param>
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137 <param name="centering" label="Compute centers for classes (e.g., treatments)" type="select" help="[default: 'none']">
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138 <option value="none" selected="true">none: &#160;&#160; Do not compute centers for classes/treatments.</option>
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139 <option value="centroid">centroid: &#160;&#160; For each class, compute the mean for each feature.</option>
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140 <option value="median">median: &#160;&#160; For each class, compute the median for each feature.</option>
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141 <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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142 </param>
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143 </inputs>
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144 <outputs>
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145 <data name="dataMatrix_out" format="tabular" label="${dataMatrix_in.name}.subset" ></data>
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146 <data name="sampleMetadata_out" format="tabular" label="${sampleMetadata_in.name}.subset" ></data>
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147 <data name="variableMetadata_out" format="tabular" label="${variableMetadata_in.name}.subset" ></data>
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148 </outputs>
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149 <tests>
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150 <!-- test 1 -->
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151 <test>
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152 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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153 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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154 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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155 <param name="classnameColumn" value="gender"/>
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156 <param name="sampleclassNames" value="M"/>
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157 <param name="wildcards" value="FALSE"/>
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158 <param name="inclusive" value="TRUE"/>
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159 <param name="variableRangeFilter" value="FEATMAX:2e6:,mz:200:,rt::800"/>
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160 <param name="transformation" value="none"/>
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161 <output name="dataMatrix_out">
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162 <assert_contents>
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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163 <has_text text="747080" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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164 <not_has_text text="13420742" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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165 <not_has_text text="47259" />
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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166 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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167 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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168 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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169 <assert_contents>
12
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_017" />
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_034" />
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_078" />
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_091" />
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_093" />
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_099" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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176 <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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177 <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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178 <has_text text="HU_138" />
10
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_028" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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180 <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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181 <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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182 <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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183 <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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184 <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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185 <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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186 <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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187 <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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188 <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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189 <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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190 </assert_contents>
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191 </output>
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192 <output name="variableMetadata_out">
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193 <assert_contents>
12
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194 <has_text text="HMDB00208" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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195 <has_text text="HMDB01032" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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196 <has_text text="HMDB01101.1" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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197 <has_text text="HMDB13189" />
10
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198 <not_has_text text="HMDB00191" />
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="HMDB00251" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
200 <not_has_text text="HMDB00299" />
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="HMDB00512" />
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="HMDB00518" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
203 <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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204 <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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205 <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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206 <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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207 <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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208 <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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209 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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210 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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211 </test>
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212 <!-- test 2 -->
14
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213 <test>
10
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214 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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215 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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216 <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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217 <!-- test that hyphens in regular expressions work -->
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218 <param name="sampleclassNames" value="HU_[0-9][0-9][0-9]"/>
12
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219 <param name="inclusive" value="TRUE"/>
10
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220 <param name="wildcards" value="FALSE"/>
12
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221 <param name="classnameColumn" value="sampleMetadata"/>
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222 <!-- test that variableRangeFilter works with tranformation -->
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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223 <param name="variableRangeFilter" value="FEATMAX:6.30103:,mz:200:,rt::800"/>
12
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224 <param name="transformation" value="log10"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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225 <param name="imputation" value="zero"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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226 <output name="dataMatrix_out" md5="5644d2ea01d072ee1d0c40e29e9d0089">
10
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227 <assert_contents>
14
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228 <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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229 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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230 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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231 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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232 <assert_contents>
12
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233 <has_text text="HU_017" />
10
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234 <has_text text="HU_028" />
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
235 <has_text text="HU_034" />
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
236 <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
237 <has_text text="HU_060" />
12
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_078" />
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
239 <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
240 <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
241 <has_text text="HU_099" />
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
242 <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
243 <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
244 <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
245 <has_text text="HU_138" />
10
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_149" />
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_152" />
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248 <has_text text="HU_175" />
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249 <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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250 <has_text text="HU_185" />
12
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251 <has_text text="HU_208" />
10
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252 <not_has_text text="HU_204" />
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253 </assert_contents>
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254 </output>
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255 <output name="variableMetadata_out">
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256 <assert_contents>
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257 <has_text text="HMDB00191" />
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258 <has_text text="HMDB00208" />
12
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259 <has_text text="HMDB01032" />
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260 <has_text text="HMDB01101.1" />
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261 <has_text text="HMDB13189" />
10
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262 <not_has_text text="HMDB00251" />
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263 <not_has_text text="HMDB00299" />
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264 <not_has_text text="HMDB00512" />
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265 <not_has_text text="HMDB00518" />
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266 <not_has_text text="HMDB00715" />
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267 <not_has_text text="HMDB00822" />
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268 <not_has_text text="HMDB03193" />
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269 <not_has_text text="HMDB04824" />
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270 <not_has_text text="HMDB10348" />
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271 <not_has_text text="HMDB59717" />
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272 </assert_contents>
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273 </output>
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274 </test>
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275 <!-- test 3 -->
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276 <test>
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277 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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278 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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279 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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280 <param name="classnameColumn" value="gender"/>
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281 <param name="sampleclassNames" value="M"/>
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282 <param name="inclusive" value="TRUE"/>
10
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283 <param name="transformation" value="none"/>
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284 <output name="dataMatrix_out">
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285 <assert_contents>
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286 <not_has_text text="HU_028" />
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287 <not_has_text text="HU_051" />
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288 <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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289 <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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290 <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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291 <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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292 <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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293 <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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294 <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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295 <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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296 <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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297 <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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298 <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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299 <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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300 <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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301 <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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302 <has_text text="HU_099" />
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303 <has_text text="HU_130" />
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304 <has_text text="HU_134" />
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305 <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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306 <has_text text="HMDB03193" />
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307 <not_has_text text="HMDB00822" />
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308 <has_text text="HMDB01101" />
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309 <has_text text="HMDB01101.1" />
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310 <has_text text="HMDB10348" />
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311 <has_text text="HMDB59717" />
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312 <has_text text="HMDB13189" />
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313 <has_text text="HMDB00299" />
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314 <has_text text="HMDB00191" />
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315 <has_text text="HMDB00518" />
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316 <has_text text="HMDB00715" />
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317 <has_text text="HMDB01032" />
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318 <has_text text="HMDB00208" />
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319 <has_text text="HMDB04824" />
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320 <has_text text="HMDB00512" />
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321 <has_text text="HMDB00251" />
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322 </assert_contents>
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323 </output>
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324 </test>
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325 <!-- test 4 -->
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326 <test>
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327 <param name="dataMatrix_in" value="input_dataMatrix.tsv"/>
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328 <param name="sampleMetadata_in" value="input_sampleMetadata.tsv"/>
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329 <param name="variableMetadata_in" value="input_variableMetadata.tsv"/>
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330 <param name="classnameColumn" value="gender"/>
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331 <param name="sampleclassNames" value="*"/>
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332 <param name="wildcards" value="TRUE"/>
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333 <param name="inclusive" value="TRUE"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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334 <param name="imputation" value="zero"/>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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335 <output name="dataMatrix_out" md5="b2eac4946d3803a07606286b50451af4">
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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336 <assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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337 <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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338 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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339 </output>
10
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340 <output name="sampleMetadata_out">
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341 <assert_contents>
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342 <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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343 <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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344 <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
345 <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
346 <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
347 <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
348 <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
349 <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
350 <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
351 <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
352 <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
353 <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
354 <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
355 <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
356 <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
357 <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
358 <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
359 <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
360 <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
361 <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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362 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
363 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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364 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
365 <!-- test 5 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
366 <test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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367 <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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368 <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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369 <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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370 <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
371 <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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372 <param name="wildcards" value="FALSE"/>
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
373 <param name="inclusive" value="TRUE"/>
10
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374 <output name="sampleMetadata_out">
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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375 <assert_contents>
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_028" />
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_051" />
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_060" />
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_110" />
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_149" />
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_152" />
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_175" />
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_178" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
384 <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
385 <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
386 <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
387 <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
388 <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
389 <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
390 <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
391 <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
392 <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
393 <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
394 <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
395 <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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396 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
397 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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398 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
399 <!-- test 6 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
400 <test>
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="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
402 <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
403 <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
404 <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
405 <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
406 <param name="wildcards" value="FALSE"/>
12
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diff changeset
407 <param name="inclusive" value="TRUE"/>
10
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diff changeset
408 <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
409 <assert_contents>
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="HMDB03193" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
411 <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
412 <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
413 <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
414 <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
415 <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
416 <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
417 <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
418 <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
419 <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
420 <has_text text="HMDB00715" />
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diff changeset
421 <has_text text="HMDB01032" />
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diff changeset
422 <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
423 <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
424 <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
425 <has_text text="HMDB00251" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
426 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
427 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
428 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
429 <!-- test 7 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
430 <test>
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="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
432 <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
433 <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
434 <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
435 <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
436 <param name="wildcards" value="FALSE"/>
12
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diff changeset
437 <param name="inclusive" value="TRUE"/>
10
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diff changeset
438 <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
439 <assert_contents>
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="HMDB03193" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
441 <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
442 <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
443 <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
444 <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
445 <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
446 <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
447 <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
448 <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
449 <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
450 <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
451 <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
452 <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
453 <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
454 <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
455 <has_text text="HMDB00251" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
456 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
457 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
458 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
459 <!-- test 8 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
460 <test>
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="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
462 <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
463 <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
464 <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
465 <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
466 <param name="wildcards" value="FALSE"/>
12
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diff changeset
467 <param name="inclusive" value="TRUE"/>
10
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diff changeset
468 <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
469 <assert_contents>
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_028" />
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_051" />
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_060" />
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_110" />
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_149" />
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_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
476 <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
477 <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
478 <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
479 <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
480 <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
481 <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
482 <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
483 <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
484 <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
485 <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
486 <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
487 <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
488 <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
489 <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
490 </assert_contents>
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diff changeset
491 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
492 </test>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
493 <!-- test 9 -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
494 <test>
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="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
496 <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
497 <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
498 <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
499 <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
500 <param name="wildcards" value="FALSE"/>
12
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diff changeset
501 <param name="inclusive" value="TRUE"/>
10
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diff changeset
502 <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
503 <assert_contents>
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_028" />
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_051" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
506 <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
507 <has_text text="HU_110" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
508 <has_text text="HU_149" />
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_152" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
510 <has_text text="HU_175" />
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_178" />
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_185" />
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
513 <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
514 <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
515 <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
516 <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
517 <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
518 <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
519 <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
520 <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
521 <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
522 <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
523 <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
524 </assert_contents>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
525 </output>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
526 </test>
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
527 <!-- 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
528 <test>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
529 <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
530 <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
531 <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
532 <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
533 <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
534 <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
535 <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
536 <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
537 <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
538 <assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
539 <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
540 <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
541 <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
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 </output>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
544 <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
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 <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
547 <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
548 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
549 </output>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
550 </test>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
551 <!-- 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
552 <test>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
553 <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
554 <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
555 <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
556 <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
557 <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
558 <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
559 <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
560 <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
561 <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
562 <assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
563 <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
564 <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
565 <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
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 </output>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
568 <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
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 <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
571 <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
572 </assert_contents>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
573 </output>
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
574 </test>
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
575 <!-- 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
576 <test>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
577 <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
578 <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
579 <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
580 <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
581 <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
582 <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
583 <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
584 <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
585 <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
586 <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
587 <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
588 <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
589 <assert_contents>
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
590 <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
591 <has_text text="4763576" />
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
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diff changeset
592 <has_text text="2003278" />
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593 <has_text text="26222916" />
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594 </assert_contents>
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595 </output>
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596 <output name="sampleMetadata_out">
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597 <assert_contents>
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598 <not_has_text text="HU_099" />
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599 <not_has_text text="HU_185" />
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600 <has_text text="HU_110" />
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601 <has_text text="HU_078" />
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602 </assert_contents>
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603 </output>
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604 </test>
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605 </tests>
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606 <help><![CDATA[
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607
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608
5
2cdf7d5982c8 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a2d17eac4a1343a34cf2908d9ab31b3202a21f64
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609 **Author** Arthur Eschenlauer (University of Minnesota, esch0041@umn.edu)
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610
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611 --------------------------------------------------------------------------
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612
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613
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614 **R package**
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615
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616 The *w4mclassfilter* package (which is used by the W4M Data Subset tool) is available from the Hegeman lab GitHub repository (https://github.com/HegemanLab/w4mclassfilter/releases).
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617
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618 -----------------------------------------------------------------------------------------------------------------------------------------
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619
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620
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621 **Tool updates**
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622
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623 See https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper#news
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624
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625 ---------------------------------------------------
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626
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627 ======================================================
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628 "W4M Data Subset" - Filter Workflow4Metabolomics data
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629 ======================================================
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630
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631 ----------
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632 Motivation
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633 ----------
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634
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635 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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636 (If a chemical is fragmented or may have a variety of adducts, several features will result.)
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637 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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638 Ideally, features would be sufficiently reproducible among sample-runs to distinguish features that are similar among samples from those that differ.
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639
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640 For liquid chromatography, the retention time for a species can vary considerably from one chromatography run to the next.
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641 The Workflow4Metabolomics suite of Galaxy tools (W4M, [Giacomoni *et al.*, 2014, Guitton *et al.* 2017])
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642 uses the XCMS preprocessing tools [Smith *et al.*, 2006]
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643 for "retention-time correction" to align features among samples.
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644 Features may be better aligned if pooled samples and blanks are included.
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645
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646 Multivariate statistical tools may be used to discover clusters of similar samples [Th]]>&#233;<![CDATA[venot *et al.*, 2015].
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647 However, once retention-time alignment of features has been achieved among samples in LC-MS datasets:
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648
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649 - The presence of pools and blanks may confound identification and separation of sample clusters.
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650 - Multivariate statistical algorithms may be impacted by missing values or dimensions that have zero variance.
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651
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652 -----------
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653 Description
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654 -----------
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655
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656 The **W4M Data Subset** tool **selects subsets of samples, features, or data values** and **conditions the data** for further analysis.
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657
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658 - 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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659 - The tool produces the same trio of output datasets, modified as described below.
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660
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661 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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662
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663 - *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.
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664 - *Feature filtering:* Features may be selected by specifying minimum or maximum value (or both) allowable in columns of *variableMetadata*.
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665 - *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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666
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667 This tool also conditions data for statistical analysis:
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668
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669 - Samples that are missing from either *sampleMetadata* or *dataMatrix* are eliminated.
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670 - Features that are missing from either *variableMetadata* or *dataMatrix* are eliminated.
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671 - Features and samples that have zero variance are eliminated.
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672 - Samples and features are ordered consistently in *variableMetadata*, *sampleMetadata*, and *dataMatrix*.
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673 (The columns for sorting *variableMetadata* or *sampleMetadata* may be specified.)
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674 - The names of the first columns of *variableMetadata* and *sampleMetadata* are set respectively to "variableMetadata" and "sampleMetadata".
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675 - If desired, the values in *dataMatrix* may be log-transformed.
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676 - Negative intensities become missing values (before missing-value replacement is performed).
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677 - If desired, each missing value in *dataMatrix* may be replaced with zero or the median value observed for the corresponding feature.
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678 - If desired, a "center" for each treatment can be computed in lieu of the samples for that treatment.
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679
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680 This tool may be applied several times sequentially, which may be useful for:
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681
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682 - analyzing subsets of samples for progressively smaller sets of treatment levels, or
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683 - choosing subsets of samples or features, respectively based on criteria in columns of *sampleMetadata* or *variableMetadata*.
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684
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685 -----------------
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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686 Workflow Position
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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687 -----------------
191a720488ce planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit dacc1bae8e60340a431907fe8a8b490357e1bfc0
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688
8
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689 This tool can be used at any point downstream of Preprocessing.
0
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690
8
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691 - Possible upstream tool categories: Preprocessing, Quality Control, Statistical Analysis, Filter and Sort
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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692 - Possible downstream tool categories: Normalisation, Statistical Analysis, Quality Control, Filter and Sort
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693
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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694 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
695 Input files
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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696 -----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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697
14
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698 +------------------------+---------------------------------------+------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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699 | File | Contents | Format |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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700 +========================+=======================================+============+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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701 | Data matrix | per-feature, per-sample intensities | tabular |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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702 +------------------------+---------------------------------------+------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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703 | Sample metadata | metadata for samples | tabular |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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704 +------------------------+---------------------------------------+------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
705 | Variable metadata | metadata for features | tabular |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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706 +------------------------+---------------------------------------+------------+
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
707
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
708
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
709 ----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
710 Parameters
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
711 ----------
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
712
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
713 Data matrix
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
714 | feature x sample **dataMatrix** (tab-separated values) file of the numeric data matrix, with period-character ('.') as decimal, and 'NA' for missing values.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
715 | The file must not contain metadata apart from the required row and column names.
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
716 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
717
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
718 Sample metadata
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
719 | 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
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
720 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
721
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
722 Variable metadata
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
723 | 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.
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
724 |
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
725
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
726 Column containing the sample-class names (default = '``class``')
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
727 | 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.
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
728 | Only letters, digits, periods, and underscores are permitted.
4
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
729 |
499c7ecfa834 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7049f74a86f6e47565a68336d6496d112713cbba
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diff changeset
730
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
731 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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diff changeset
732 | names (or regular expressions to match names) of sample-classes to include or exclude
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
733 | (Separate names with commas, without any extra space characters.)
0
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diff changeset
734 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
735
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
736 Exclude/include named (or matched) classes (default = '``filter-out``')
8
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
737 | '``filter-in``' - include only the named sample-classes
d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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diff changeset
738 | '``filter-out``' - exclude only the named sample-classes
0
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diff changeset
739 |
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
740
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
741 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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diff changeset
742 | '``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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diff changeset
743 | '``regular-expression patterns``' - use regular expressions to match the named sample-classes (see the *'Regular-expression patterns to match class names'* section below.)
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
744 |
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
745
14
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diff changeset
746 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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diff changeset
747 | 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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diff changeset
748 | (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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diff changeset
749 |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
750
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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751 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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752 | '``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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753 | '``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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754 | '``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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755 |
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756 | 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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757 |
12
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diff changeset
758
14
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diff changeset
759 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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760 | '``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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761 | '``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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762 | '``center``' - For each feature, negative and missing values are imputed to the median of other values.
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d5cf23369d12 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 7b824bc01884125dc8bb2e4c9ef70fb0a6d88db1
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763 |
14
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diff changeset
764 | 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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765 |
0
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766
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
767 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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768 | 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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769 | (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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770 |
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
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diff changeset
771
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87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
772 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
773 | 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
774 | (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
775 |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
776
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777 Compute centers for classes, e.g., treatments (default = '``none``')
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778 | '``none``' - Return all samples; do not compute centers for classes/treatments.
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779 | '``centroid``' - For each treatment, return only the centroid (the treatment-center computed as the mean intensity for each feature).
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780 | '``median``' - For each treatment, return only the treatment-center computed as the median intensity for each feature.
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781 | '``medoid``' - For each treatment, return only the medoid (the sample most similar to the other samples for that treatment).
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782 |
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783 | Note well: For '``medoid``' option, '``Imputation of missing values``' cannot be set to '``none``'.
13
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784 |
0
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785
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786 ------------
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787 Output files
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788 ------------
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789
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790 sampleMetadata
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791 | (tab-separated values) file.
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792 | 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)
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793 | If centering is '``centroid``' or '``median``', most columns will be replaced with the treatment name and the number of samples for that treatment.
0
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794 |
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795
2
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796 variableMetadata
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797 | (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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798 |
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799
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800 dataMatrix
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801 | (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
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802 |
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803
2
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804
8
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805 -----------------------------------------
14
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diff changeset
806 Wild-card patterns to match class names
8
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807 -----------------------------------------
4
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808
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809 W4M Data Subset supports use of "wild card" patterns to select class-names.
4
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810
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811 - use '``?``' to match a single character
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812 - use '``*``' to match zero or more characters
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813 - the entire pattern must match the sample name
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814
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815 For example
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816
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817 - '``??.samp*``' matches '``my.sample``' but not '``my.own.sample``'
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818 - '``*.sample``' matches '``my.sample``' and '``my.own.sample``'
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819 - '``*.sampl``' matches neither '``my.sample``' nor '``my.own.sample``'
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820
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821 --------------------------------------------------
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822 Regular-expression patterns to match class names
8
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823 --------------------------------------------------
4
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824
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825 W4M Data Subset supports use of R "extended regular expression" patterns to select class-names.
4
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826
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827 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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828 https://stat.ethz.ch/R-manual/R-devel/library/base/html/regex.html
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829
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830 However, only a few basic building blocks of regular expressions need to be mastered for most cases:
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831
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832 - '``^``' matches the beginning of a class-name
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833 - '``$``' matches the end of a class-name
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834 - '``.``' outside of square brackets matches a single character
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835 - '``*``' matches character specified immediately before zero or more times
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836 - square brackets specify a set of characters to be matched.
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837
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838 Within square brackets
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839
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840 - '``^``' as the first character specifies that the list of characters are those that should **not** be matched.
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841 - '``-``' is used to specify ranges of characters
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842
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843 Caveat: The tool wrapper uses the comma ('``,``') to split a list of sample-class names, so **commas may not be used within regular expressions for this tool**
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844
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845 First Example: Consider a field of class-names consisting of '``marq3,marq6,marq9,marq12,front3,front6,front9,front12``'
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846
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847 - The regular expression '``^front[0-9][0-9]*$``' will match the same sample-classes as '``front3,front6,front9,front12``'
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848 - The regular expression '``^[a-z][a-z]3$``' will match the same sample-classes as '``front3,marq3``'
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849 - The regular expression '``^[a-z][a-z]12$``' will match the same sample-classes as '``front12,marq12``'
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850 - The regular expression '``^[a-z][a-z][0-9]$``' will match the same sample-classes as '``front3,front6,front9,marq3,marq6,marq9``'
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851
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852 Second Example: Consider these regular expression patterns as possible matches to a sample-class name '``AB0123``':
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853
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854 - '``^[A-Z][A-Z][0-9][0-9]*$``' MATCHES '``**^AB0123$**``'
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855 - '``^[A-Z][A-Z]*[0-9][0-9]*$``' MATCHES '``**^AB0123$**``'
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856 - '``^[A-Z][0-9]*``' MATCHES '``**^A** B0123$``' - first character is a letter, '``*``' can specify zero characters, and end of line did not need to be matched.
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857 - '``^[A-Z][A-Z][0-9]``' MATCHES '``**^AB0** 123$``' - first two characters are letters aind the third is a digit.
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858 - '``^[A-Z][A-Z]*[0-9][0-9]$``' DOES NOT MATCH - the name does not end with the pattern '``[A-Z][0-9][0-9]$``', i.e., it ends with four digits, not two.
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859 - '``^[A-Z][0-9]*$``' DOES NOT MATCH - the pattern specifies that second character and all those that follow, if present, must be digits.
4
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860
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861 ----------------------
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862 Variable-range filters
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863 ----------------------
4
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864
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865 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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866 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"
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diff changeset
867 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
868 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
869 following order:
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
870
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87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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871 - 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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diff changeset
872 - 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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873 - the **maximum allowed value**, e.g., '``800``'.
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
874
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649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
875 Note for the range specification strings:
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
876
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87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
877 - **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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878 - **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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diff changeset
879
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diff changeset
880 - 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"
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diff changeset
881 - 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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diff changeset
882
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
883 ----------------------------------
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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884 Data transformation and imputation
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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885 ----------------------------------
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
886
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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887 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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diff changeset
888
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889 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"
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diff changeset
890
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
891 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"
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diff changeset
892
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
893 - 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"
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diff changeset
894 - 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"
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diff changeset
895
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
896 - 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"
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diff changeset
897
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
898 -----------------------------------------
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
899 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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900 -----------------------------------------
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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901
14
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902 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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diff changeset
903
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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904 - '``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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905 - '``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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diff changeset
906 - '``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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907 - '``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"
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parents: 13
diff changeset
908
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 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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diff changeset
910
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
911 - 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"
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parents: 13
diff changeset
912 - 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"
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diff changeset
913 - 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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diff changeset
914
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
915 -----------------------------------------------------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
916
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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parents: 5
diff changeset
917 ----------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
918 WORKING EXAMPLES
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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919 ----------------
2
23c6d271def9 planemo upload
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diff changeset
920
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
921 -----------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
922 Input Files
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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923 -----------
2
23c6d271def9 planemo upload
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diff changeset
924
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
925 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
926 | Input File URL |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
927 +======================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
928 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_dataMatrix.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
929 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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930 | https://raw.githubusercontent.com/HegemanLab/w4mclassfilter_galaxy_wrapper/master/tools/w4mclassfilter/test-data/input_sampleMetadata.tsv |
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
931 +------------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
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diff changeset
932 | 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
933 +------------------------------------------------------------------------------------------------------------------------------------------------------+
2
23c6d271def9 planemo upload
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diff changeset
934
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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935 -------------------------------
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
936 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
937 -------------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
938
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
939 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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diff changeset
940
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
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diff changeset
941 **Input parameters**
0
bab3a658f74e planemo upload commit 91805bf8e8ce26193ffc4cc2f3dca56ce4addf79
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diff changeset
942
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
943 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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944 | Input Parameter | Value |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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945 +=============================================+===============================+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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946 | 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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947 +---------------------------------------------+-------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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948 | Sample-class names | M |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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diff changeset
949 +---------------------------------------------+-------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
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950 | Exclude/include named classes | filter-in |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
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diff changeset
951 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
952 | Use 'wild-cards' or 'regular expressions' | wild-cards |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
953 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
954 | 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
955 +---------------------------------------------+-------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
956 | Data transformation | none |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
957 +---------------------------------------------+-------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
958 | Missing-value imputation | center |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
959 +---------------------------------------------+-------------------------------+
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
eschen42
parents: 12
diff changeset
960 | 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
961 +---------------------------------------------+-------------------------------+
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
eschen42
parents: 12
diff changeset
962 | 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
963 +---------------------------------------------+-------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
964 | 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
965 +---------------------------------------------+-------------------------------+
2
23c6d271def9 planemo upload
eschen42
parents: 0
diff changeset
966
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
967 **Expected outputs**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
968
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
969 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
970 | 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
971 +===================+=================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
972 | 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
eschen42
parents: 9
diff changeset
973 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
974 | 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
eschen42
parents: 9
diff changeset
975 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
976 | 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
eschen42
parents: 9
diff changeset
977 +-------------------+-------------------------------------------------------------------------------------------------------------------------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
978
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
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 Example with Range-Filtering
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
981 ----------------------------
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
982
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
983 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
eschen42
parents: 5
diff changeset
984 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
eschen42
parents: 5
diff changeset
985
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
986 **Input parameters**
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
987
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
988 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
989 | Input Parameter | Value |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
990 +=============================================+===================================+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
991 | Column that names the sample class | sampleMetadata |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
992 +---------------------------------------------+-----------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
993 | Sample-class names | HU_13[48] |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
994 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
995 | Exclude/include named classes | filter-out |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
996 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
997 | Use 'wild-cards' or 'regular expressions' | regular-expressions |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
998 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
999 | 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"
eschen42
parents: 11
diff changeset
1000 +---------------------------------------------+-----------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1001 | Data transformation | log2 |
12
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
1002 +---------------------------------------------+-----------------------------------+
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
1003 | Missing-value imputation | zero |
38f509903a0b "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit b9712e554d16ed26f6c6d0c2e8cd74552b49f694"
eschen42
parents: 11
diff changeset
1004 +---------------------------------------------+-----------------------------------+
13
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
eschen42
parents: 12
diff changeset
1005 | 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
1006 +---------------------------------------------+-----------------------------------+
c18040b6e8b9 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 1a5dd14c3697516bc55950bd6e46c978af7c19cf"
eschen42
parents: 12
diff changeset
1007 | 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
1008 +---------------------------------------------+-----------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1009 | 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
1010 +---------------------------------------------+-----------------------------------+
6
38ccf6722d54 planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a06ae79d25b31d02217b934b9cd61a5aba3f640f
eschen42
parents: 5
diff changeset
1011
2
23c6d271def9 planemo upload
eschen42
parents: 0
diff changeset
1012 **Expected outputs**
23c6d271def9 planemo upload
eschen42
parents: 0
diff changeset
1013
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1014 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1015 | 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
1016 +===================+===================================================================================================================================================+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1017 | 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
1018 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1019 | 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
1020 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1021 | 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
1022 +-------------------+---------------------------------------------------------------------------------------------------------------------------------------------------+
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1023
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1024 --------------------------------
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1025 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
1026 --------------------------------
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1027
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1028 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
1029
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1030 **Input parameters**
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1031
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1032 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1033 | Input Parameter | Value |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1034 +=============================================+===================================+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1035 | 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
1036 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1037 | 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
1038 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1039 | 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
1040 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1041 | 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
1042 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1043 | 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
1044 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1045 | Data transformation | none |
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1046 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1047 | 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
1048 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1049 | 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
1050 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1051 | 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
1052 +---------------------------------------------+-----------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1053 | 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
1054 +---------------------------------------------+-----------------------------------+
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 **Expected outputs**
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1057
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 | 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
1060 +===================+==========================================================================================================+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1061 | 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
1062 +-------------------+----------------------------------------------------------------------------------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1063 | 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
1064 +-------------------+----------------------------------------------------------------------------------------------------------+
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1065 | 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
1066 +-------------------+----------------------------------------------------------------------------------------------------------+
10
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1067 ]]></help>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1068 <citations>
14
87ec0d3c2266 "planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit a9664e9a04e49d436ebbb643ba1755397ab759dc"
eschen42
parents: 13
diff changeset
1069 <!-- 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
1070 <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
1071 <!-- 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
1072 <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
1073 <!-- Kuhl_2012 CAMERA -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1074 <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
1075 <!-- Smith_2006 XCMS -->
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1076 <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
1077 <!-- 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
1078 <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
1079 </citations>
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1080 <!--
649cb1bafd3e planemo upload for repository https://github.com/HegemanLab/w4mclassfilter_galaxy_wrapper/tree/master commit 830e149719d947099da61dcc288aa03a97663b5c
eschen42
parents: 9
diff changeset
1081 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
1082 --> </tool>