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1 <?xml version="1.0" ?>
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2 <tool id="qiime_sample-classifier_classify-samples" name="qiime sample-classifier classify-samples" version="2019.7">
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3 <description> - Train and test a cross-validated supervised learning classifier.</description>
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4 <requirements>
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5 <requirement type="package" version="2019.7">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime sample-classifier classify-samples
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9
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10 --i-table=$itable
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11 --m-metadata-column="$mmetadatacolumn"
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12
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5
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13 #if str($ptestsize):
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14 --p-test-size=$ptestsize
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15 #end if
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16
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5
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17 #if str($pstep):
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18 --p-step=$pstep
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19 #end if
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20
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5
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21 #if str($pcv):
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22 --p-cv=$pcv
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23 #end if
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24
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25 #if str($prandomstate):
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26 --p-random-state="$prandomstate"
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27 #end if
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28
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29 #set $pnjobs = '${GALAXY_SLOTS:-4}'
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30
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31 #if str($pnjobs):
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32 --p-n-jobs="$pnjobs"
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33 #end if
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34
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35
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36 #if $pnestimators:
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37 --p-n-estimators=$pnestimators
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38 #end if
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39
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40 #if str($pestimator) != 'None':
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41 --p-estimator=$pestimator
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42 #end if
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43
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44 #if $poptimizefeatureselection:
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45 --p-optimize-feature-selection
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46 #end if
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47
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48 #if $pparametertuning:
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49 --p-parameter-tuning
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50 #end if
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51
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52 #if str($ppalette) != 'None':
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53 --p-palette=$ppalette
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54 #end if
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55
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56 #if str($pmissingsamples) != 'None':
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57 --p-missing-samples=$pmissingsamples
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58 #end if
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59
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60
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61 #if $metadatafile:
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62 --m-metadata-file=$metadatafile
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63 #end if
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64
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65
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66
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67 --o-probabilities=oprobabilities
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68 --o-sample-estimator=osampleestimator
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69 --o-feature-importance=ofeatureimportance
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70 --o-predictions=opredictions
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71 --o-model-summary=omodelsummary
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72 --o-accuracy-results=oaccuracyresults
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73 ;
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74 cp oprobabilities.qza $oprobabilities;
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75 cp osampleestimator.qza $osampleestimator;
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76 cp ofeatureimportance.qza $ofeatureimportance;
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77 cp opredictions.qza $opredictions;
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78 qiime tools export --input-path omodelsummary.qzv --output-path out && mkdir -p '$omodelsummary.files_path'
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79 && cp -r out/* '$omodelsummary.files_path'
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80 && mv '$omodelsummary.files_path/index.html' '$omodelsummary';
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81 qiime tools export --input-path oaccuracyresults.qzv --output-path out && mkdir -p '$oaccuracyresults.files_path'
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82 && cp -r out/* '$oaccuracyresults.files_path'
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83 && mv '$oaccuracyresults.files_path/index.html' '$oaccuracyresults'
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84 ]]></command>
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85 <inputs>
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86 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction. [required]" name="itable" optional="False" type="data"/>
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87 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical metadata column to use as prediction target. [required]" name="mmetadatacolumn" optional="False" type="text"/>
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88 <param label="--p-test-size: PROPORTION Range(0.0, 1.0, inclusive_start=False) Fraction of input samples to exclude from training set and use for classifier testing. [default: 0.2]" name="ptestsize" optional="True" type="float" value="0.2" min="0" max="1" exclusive_start="True"/>
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89 <param label="--p-step: PROPORTION Range(0.0, 1.0, inclusive_start=False) If optimize-feature-selection is True, step is the percentage of features to remove at each iteration. [default: 0.05]" name="pstep" optional="True" type="float" value="0.05" min="0" max="1" exclusive_start="True"/>
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90 <param label="--p-cv: INTEGER Number of k-fold cross-validations to perform. Range(1, None) [default: 5]" name="pcv" optional="True" type="integer" value="5" min="1"/>
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91 <param label="--p-random-state: INTEGER Seed used by random number generator. [optional]" name="prandomstate" optional="True" type="integer"/>
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92 <param label="--p-n-estimators: INTEGER Range(1, None) Number of trees to grow for estimation. More trees will improve predictive accuracy up to a threshold level, but will also increase time and memory requirements. This parameter only affects ensemble estimators, such as Random Forest, AdaBoost, ExtraTrees, and GradientBoosting. [default: 100]" name="pnestimators" optional="True" type="integer" value="100" min="1"/>
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93 <param label="--p-estimator: " name="pestimator" optional="True" type="select">
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94 <option selected="True" value="None">Selection is Optional</option>
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95 <option value="RandomForestClassifier">RandomForestClassifier</option>
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96 <option value="ExtraTreesClassifier">ExtraTreesClassifier</option>
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97 <option value="GradientBoostingClassifier">GradientBoostingClassifier</option>
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98 <option value="AdaBoostClassifier">AdaBoostClassifier</option>
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99 <option value="KNeighborsClassifier">KNeighborsClassifier</option>
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100 <option value="LinearSVC">LinearSVC</option>
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101 <option value="SVC">SVC</option>
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102 </param>
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103 <param label="--p-optimize-feature-selection: --p-no-optimize-feature-selection Automatically optimize input feature selection using recursive feature elimination. [default: False]" name="poptimizefeatureselection" selected="False" type="boolean"/>
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104 <param label="--p-parameter-tuning: --p-no-parameter-tuning Automatically tune hyperparameters using random grid search. [default: False]" name="pparametertuning" selected="False" type="boolean"/>
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105 <param label="--p-palette: " name="ppalette" optional="True" type="select">
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106 <option selected="True" value="None">Selection is Optional</option>
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107 <option value="YellowOrangeBrown">YellowOrangeBrown</option>
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108 <option value="YellowOrangeRed">YellowOrangeRed</option>
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109 <option value="OrangeRed">OrangeRed</option>
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110 <option value="PurpleRed">PurpleRed</option>
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111 <option value="RedPurple">RedPurple</option>
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112 <option value="BluePurple">BluePurple</option>
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113 <option value="GreenBlue">GreenBlue</option>
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114 <option value="PurpleBlue">PurpleBlue</option>
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115 <option value="YellowGreen">YellowGreen</option>
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116 <option value="summer">summer</option>
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117 <option value="copper">copper</option>
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118 <option value="viridis">viridis</option>
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119 <option value="plasma">plasma</option>
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120 <option value="inferno">inferno</option>
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121 <option value="magma">magma</option>
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122 <option value="sirocco">sirocco</option>
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123 <option value="drifting">drifting</option>
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124 <option value="melancholy">melancholy</option>
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125 <option value="enigma">enigma</option>
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126 <option value="eros">eros</option>
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127 <option value="spectre">spectre</option>
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128 <option value="ambition">ambition</option>
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129 <option value="mysteriousstains">mysteriousstains</option>
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130 <option value="daydream">daydream</option>
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131 <option value="solano">solano</option>
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132 <option value="navarro">navarro</option>
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133 <option value="dandelions">dandelions</option>
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134 <option value="deepblue">deepblue</option>
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135 <option value="verve">verve</option>
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136 <option value="greyscale">greyscale</option>
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137 </param>
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138 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
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139 <option selected="True" value="None">Selection is Optional</option>
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140 <option value="error">error</option>
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141 <option value="ignore">ignore</option>
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142 </param>
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143
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144 <param label="--m-metadata-file METADATA" name="metadatafile" type="data" format="tabular,qza,no_unzip.zip" />
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145
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146 </inputs>
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147 <outputs>
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148 <data format="qza" label="${tool.name} on ${on_string}: probabilities.qza" name="oprobabilities"/>
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149 <data format="qza" label="${tool.name} on ${on_string}: sampleestimator.qza" name="osampleestimator"/>
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150 <data format="qza" label="${tool.name} on ${on_string}: featureimportance.qza" name="ofeatureimportance"/>
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151 <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions"/>
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152 <data format="html" label="${tool.name} on ${on_string}: modelsummary.qzv" name="omodelsummary"/>
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153 <data format="html" label="${tool.name} on ${on_string}: accuracyresults.qzv" name="oaccuracyresults"/>
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154 </outputs>
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155 <help><![CDATA[
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156 Train and test a cross-validated supervised learning classifier.
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157 ################################################################
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158
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159 Predicts a categorical sample metadata column using a supervised learning
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160 classifier. Splits input data into training and test sets. The training set
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161 is used to train and test the estimator using a stratified k-fold cross-
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162 validation scheme. This includes optional steps for automated feature
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163 extraction and hyperparameter optimization. The test set validates
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164 classification accuracy of the optimized estimator. Outputs classification
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165 results for test set. For more details on the learning algorithm, see
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166 http://scikit-learn.org/stable/supervised_learning.html
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167
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168 Parameters
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169 ----------
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170 table : FeatureTable[Frequency]
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171 Feature table containing all features that should be used for target
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172 prediction.
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173 metadata : MetadataColumn[Categorical]
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174 Categorical metadata column to use as prediction target.
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175 test_size : Float % Range(0.0, 1.0, inclusive_start=False), optional
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176 Fraction of input samples to exclude from training set and use for
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177 classifier testing.
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178 step : Float % Range(0.0, 1.0, inclusive_start=False), optional
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179 If optimize_feature_selection is True, step is the percentage of
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180 features to remove at each iteration.
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181 cv : Int % Range(1, None), optional
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182 Number of k-fold cross-validations to perform.
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183 random_state : Int, optional
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184 Seed used by random number generator.
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185 n_estimators : Int % Range(1, None), optional
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186 Number of trees to grow for estimation. More trees will improve
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187 predictive accuracy up to a threshold level, but will also increase
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188 time and memory requirements. This parameter only affects ensemble
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189 estimators, such as Random Forest, AdaBoost, ExtraTrees, and
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190 GradientBoosting.
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191 estimator : Str % Choices('RandomForestClassifier', 'ExtraTreesClassifier', 'GradientBoostingClassifier', 'AdaBoostClassifier', 'KNeighborsClassifier', 'LinearSVC', 'SVC'), optional
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192 Estimator method to use for sample prediction.
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193 optimize_feature_selection : Bool, optional
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194 Automatically optimize input feature selection using recursive feature
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195 elimination.
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196 parameter_tuning : Bool, optional
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197 Automatically tune hyperparameters using random grid search.
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198 palette : Str % Choices('YellowOrangeBrown', 'YellowOrangeRed', 'OrangeRed', 'PurpleRed', 'RedPurple', 'BluePurple', 'GreenBlue', 'PurpleBlue', 'YellowGreen', 'summer', 'copper', 'viridis', 'plasma', 'inferno', 'magma', 'sirocco', 'drifting', 'melancholy', 'enigma', 'eros', 'spectre', 'ambition', 'mysteriousstains', 'daydream', 'solano', 'navarro', 'dandelions', 'deepblue', 'verve', 'greyscale'), optional
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199 The color palette to use for plotting.
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200 missing_samples : Str % Choices('error', 'ignore'), optional
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201 How to handle missing samples in metadata. "error" will fail if missing
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202 samples are detected. "ignore" will cause the feature table and
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203 metadata to be filtered, so that only samples found in both files are
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204 retained.
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205
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206 Returns
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207 -------
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208 sample_estimator : SampleEstimator[Classifier]
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209 Trained sample estimator.
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210 feature_importance : FeatureData[Importance]
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211 Importance of each input feature to model accuracy.
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212 predictions : SampleData[ClassifierPredictions]
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213 Predicted target values for each input sample.
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214 model_summary : Visualization
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215 Summarized parameter and (if enabled) feature selection information for
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216 the trained estimator.
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217 accuracy_results : Visualization
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218 Accuracy results visualization.
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219 probabilities : SampleData[Probabilities]
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220 Predicted class probabilities for each input sample.
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221 ]]></help>
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222 <macros>
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223 <import>qiime_citation.xml</import>
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224 </macros>
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225 <expand macro="qiime_citation"/>
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226 </tool>
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