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1 <?xml version="1.0" ?>
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2 <tool id="qiime_sample-classifier_classify-samples-ncv" name="qiime sample-classifier classify-samples-ncv"
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3 version="2020.8">
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4 <description>Nested cross-validated supervised learning classifier.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime sample-classifier classify-samples-ncv
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10
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11 --i-table=$itable
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12 # if $input_files_mmetadatafile:
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13 # def list_dict_to_string(list_dict):
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14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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15 # for d in list_dict[1:]:
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16 # set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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17 # end for
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18 # return $file_list
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19 # end def
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20 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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21 # end if
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22
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23 #if '__ob__' in str($mmetadatacolumn):
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24 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
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25 #set $mmetadatacolumn = $mmetadatacolumn_temp
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26 #end if
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27 #if '__cb__' in str($mmetadatacolumn):
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28 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
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29 #set $mmetadatacolumn = $mmetadatacolumn_temp
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30 #end if
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31 #if 'X' in str($mmetadatacolumn):
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32 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
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33 #set $mmetadatacolumn = $mmetadatacolumn_temp
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34 #end if
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35 #if '__sq__' in str($mmetadatacolumn):
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36 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
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37 #set $mmetadatacolumn = $mmetadatacolumn_temp
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38 #end if
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39 #if '__db__' in str($mmetadatacolumn):
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40 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
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41 #set $mmetadatacolumn = $mmetadatacolumn_temp
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42 #end if
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43
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44 --m-metadata-column=$mmetadatacolumn
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45
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46
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47 --p-cv=$pcv
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48
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49 #if str($prandomstate):
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50 --p-random-state=$prandomstate
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51 #end if
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52 --p-n-jobs=$pnjobs
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53
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54 --p-n-estimators=$pnestimators
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55
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56 #if str($pestimator) != 'None':
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57 --p-estimator=$pestimator
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58 #end if
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59
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60 #if $pparametertuning:
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61 --p-parameter-tuning
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62 #end if
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63
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64 #if str($pmissingsamples) != 'None':
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65 --p-missing-samples=$pmissingsamples
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66 #end if
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67
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68 --o-predictions=opredictions
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69
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70 --o-feature-importance=ofeatureimportance
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71
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72 --o-probabilities=oprobabilities
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73
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74 #if str($examples) != 'None':
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75 --examples=$examples
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76 #end if
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77
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78 ;
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79 cp oprobabilities.qza $oprobabilities
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80
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81 ]]></command>
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82 <inputs>
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83 <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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84 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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85 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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86 </repeat>
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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-cv: INTEGER Number of k-fold cross-validations to perform. Range(1, None) [default: 5]" min="1" name="pcv" optional="True" type="integer" value="5" />
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89 <param label="--p-random-state: INTEGER Seed used by random number generator. [optional]" name="prandomstate" optional="False" type="text" />
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90 <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]" min="1" name="pnestimators" optional="True" type="integer" value="100" />
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91 <param label="--p-estimator: " name="pestimator" optional="True" type="select">
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92 <option selected="True" value="None">Selection is Optional</option>
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93 <option value="RandomForestClassifier">RandomForestClassifier</option>
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94 <option value="ExtraTreesClassifier">ExtraTreesClassifier</option>
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95 <option value="GradientBoostingClassifier">GradientBoostingClassifier</option>
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96 <option value="AdaBoostClassifier">AdaBoostClassifier</option>
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97 <option value="KNeighborsClassifier">KNeighborsClassifier</option>
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98 <option value="LinearSVC">LinearSVC</option>
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99 <option value="SVC">SVC</option>
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100 </param>
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101 <param label="--p-parameter-tuning: --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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102 <param label="--p-missing-samples: " name="pmissingsamples" optional="True" type="select">
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103 <option selected="True" value="None">Selection is Optional</option>
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104 <option value="error">error</option>
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105 <option value="ignore">ignore</option>
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106 </param>
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107 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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108
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109 </inputs>
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110
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111 <outputs>
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112 <data format="qza" label="${tool.name} on ${on_string}: predictions.qza" name="opredictions" />
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113 <data format="qza" label="${tool.name} on ${on_string}: featureimportance.qza" name="ofeatureimportance" />
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114 <data format="qza" label="${tool.name} on ${on_string}: probabilities.qza" name="oprobabilities" />
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115
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116 </outputs>
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117
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118 <help><![CDATA[
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119 Nested cross-validated supervised learning classifier.
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120 ###############################################################
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121
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122 Predicts a categorical sample metadata column using a supervised learning
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123 classifier. Uses nested stratified k-fold cross validation for automated
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124 hyperparameter optimization and sample prediction. Outputs predicted values
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125 for each input sample, and relative importance of each feature for model
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126 accuracy.
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127
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128 Parameters
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129 ----------
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130 table : FeatureTable[Frequency]
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131 Feature table containing all features that should be used for target
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132 prediction.
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133 metadata : MetadataColumn[Categorical]
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134 Categorical metadata column to use as prediction target.
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135 cv : Int % Range(1, None), optional
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136 Number of k-fold cross-validations to perform.
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137 random_state : Int, optional
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138 Seed used by random number generator.
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139 n_jobs : Int, optional
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140 Number of jobs to run in parallel.
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141 n_estimators : Int % Range(1, None), optional
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142 Number of trees to grow for estimation. More trees will improve
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143 predictive accuracy up to a threshold level, but will also increase
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144 time and memory requirements. This parameter only affects ensemble
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145 estimators, such as Random Forest, AdaBoost, ExtraTrees, and
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146 GradientBoosting.
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147 estimator : Str % Choices('RandomForestClassifier', 'ExtraTreesClassifier', 'GradientBoostingClassifier', 'AdaBoostClassifier', 'KNeighborsClassifier', 'LinearSVC', 'SVC'), optional
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148 Estimator method to use for sample prediction.
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149 parameter_tuning : Bool, optional
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150 Automatically tune hyperparameters using random grid search.
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151 missing_samples : Str % Choices('error', 'ignore'), optional
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152 How to handle missing samples in metadata. "error" will fail if missing
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153 samples are detected. "ignore" will cause the feature table and
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154 metadata to be filtered, so that only samples found in both files are
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155 retained.
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156
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157 Returns
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158 -------
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159 predictions : SampleData[ClassifierPredictions]
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160 Predicted target values for each input sample.
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161 feature_importance : FeatureData[Importance]
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162 Importance of each input feature to model accuracy.
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163 probabilities : SampleData[Probabilities]
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164 Predicted class probabilities for each input sample.
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165 ]]></help>
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166 <macros>
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167 <import>qiime_citation.xml</import>
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168 </macros>
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169 <expand macro="qiime_citation"/>
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170 </tool> |
