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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
author bgruening
date Wed, 23 Jul 2025 07:49:41 +0000
parents 466b593fd87e
children
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98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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1 <tool id="flexynesis" name="Flexynesis" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>A deep-learning based multi-omics bulk sequencing data integration suite</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="edam"/>
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7 <expand macro="requirements"/>
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8 <required_files>
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9 <include path="flexynesis_plot.py" />
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10 <include path="flexynesis_utils.py" />
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11 <include path="convert.py" />
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12 <include path="index_to_name.py" />
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13 </required_files>
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14 <command detect_errors="exit_code"><![CDATA[
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15 @CHECK_NON_COMMERCIAL_USE@
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16 mkdir -p input/test input/train output &&
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17 ln -s '$train_clin' input/train/clin.tabular &&
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18 python '$__tool_directory__/convert.py' input/train/clin.tabular input/train/clin.csv &&
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20 ln -s '$test_clin' input/test/clin.tabular &&
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21 python '$__tool_directory__/convert.py' input/test/clin.tabular input/test/clin.csv &&
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23 #if str($assay_main) != '':
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24 #set $name = str($assay_main.replace(" ", "_"))
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25 ln -s '$train_omics_main' input/train/${name}.tabular &&
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26 python '$__tool_directory__/convert.py' input/train/${name}.tabular input/train/${name}.csv &&
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28 ln -s '$test_omics_main' input/test/${name}.tabular &&
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29 python '$__tool_directory__/convert.py' input/test/${name}.tabular input/test/${name}.csv &&
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30
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31 #set $data_names = [$name]
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32 #else
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33 ln -s '$train_omics_main' input/train/main.tabular &&
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34 python '$__tool_directory__/convert.py' input/train/main.tabular input/train/main.csv &&
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35 ln -s '$test_omics_main' input/test/main.tabular &&
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36 python '$__tool_directory__/convert.py' input/test/main.tabular input/test/main.csv &&
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37 #set $data_names = ['main']
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38 #end if
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39 #if str($training_type.model) == 'cm_train':
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40 #if str($layer_main) == 'input':
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41 #set $input_layers = $data_names
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42 #set $output_layers = []
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43 #else
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44 #set $input_layers = []
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45 #set $output_layers = $data_names
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46 #end if
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47 #end if
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48 #for $i, $element in enumerate($omics)
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49 #if str($element.train_omics) != 'None' and str($element.test_omics) != 'None':
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50 #if str($element.assay) != '':
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51 #set $i = str($element.assay.replace(" ", "_"))
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52 ln -s '${element.train_omics}' input/train/${i}.tabular &&
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53 python '$__tool_directory__/convert.py' input/train/${i}.tabular input/train/${i}.csv &&
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54
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55 ln -s '${element.test_omics}' input/test/${i}.tabular &&
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56 python '$__tool_directory__/convert.py' input/test/${i}.tabular input/test/${i}.csv &&
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57
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58 $data_names.append(str($i))
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59 #if str($training_type.model) == 'cm_train':
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60 #if str($element.layer) == 'input':
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61 $input_layers.append(str($i))
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62 #else
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63 $output_layers.append(str($i))
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64 #end if
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65 #end if
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66 #else
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67 ln -s '${element.train_omics}' input/train/omics_${i}.tabular &&
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68 python '$__tool_directory__/convert.py' input/train/omics_${i}.tabular input/train/omics_${i}.csv &&
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70 ln -s '${element.test_omics}' input/test/omics_${i}.tabular &&
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71 python '$__tool_directory__/convert.py' input/test/omics_${i}.tabular input/test/omics_${i}.csv &&
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73 $data_names.append("omics_" + str($i))
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74 #if str($training_type.model) == 'cm_train':
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75 #if str($element.layer) == 'input':
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76 $input_layers.append("omics_" + str($i))
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77 #else
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78 $output_layers.append("omics_" + str($i))
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79 #end if
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80 #end if
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81 #end if
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82 #end if
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83 #end for
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84 #if str($training_type.model) == 's_train':
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85 ## set target variables
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86 #if str($target_variables) != 'None':
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87 targets=`'$__tool_directory__/index_to_name.py' input/train/clin.csv $target_variables` &&
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88 echo "Target variables: \$targets" &&
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89 #end if
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90 ## set survival variables
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91 #if str($surv_event_var) != 'None' and str($surv_time_var) != 'None':
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92 survival_event=`'$__tool_directory__/index_to_name.py' input/train/clin.csv $surv_event_var` &&
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93 ## check if survival variable is numerical
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94 echo "Survival event variable: \$survival_event" &&
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95 python '$__tool_directory__/flexynesis_utils.py' --util validate_survival --clin input/train/clin.csv --clin_variable \$survival_event &&
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96 survival_time=`$__tool_directory__/index_to_name.py input/train/clin.csv $surv_time_var` &&
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97 echo "Survival time variable: \$survival_time" &&
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98 #end if
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99 ## set clinical variables for Cox model
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100 #if str($plot.plot_cox_conditional.plot_cox) == 'yes':
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101 #if str($plot.plot_cox_conditional.clinical_variables) != 'None':
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102 covars=`'$__tool_directory__/index_to_name.py' input/train/clin.csv $plot.plot_cox_conditional.clinical_variables` &&
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103 ## check if covariates is numerical
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104 echo "Clinical variables for Cox model: \$covars" &&
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105 python '$__tool_directory__/flexynesis_utils.py' --util validate_covariate --clin input/train/clin.csv --clin_variable \$covars &&
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106 #end if
5
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107 #end if
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108 #end if
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109
3
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110 flexynesis
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111 --data_path input
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112 --outdir output
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113 --model_class $model_class
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114 #if str($model_class) == 'GNN':
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115 --gnn_conv_type $gnn_conv_type
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116 --string_organism $string_organism
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117 --string_node_name $string_node_name
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118 #end if
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119 #if str($training_type.model) == 's_train':
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120 #if str($target_variables) != 'None':
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121 --target_variables \$targets
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122 #end if
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123 #if str($surv_event_var) != 'None' and str($surv_time_var) != 'None':
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124 --surv_event_var \$survival_event
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125 --surv_time_var \$survival_time
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126 #end if
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127 #end if
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128 #if str($training_type.model) == 'cm_train':
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129 --input_layers $str(",".join($input_layers))
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130 --output_layers $str(",".join($output_layers))
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131 #end if
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132 --fusion_type $fusion_type
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133 --hpo_iter $hpo_iter
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134 --val_size $val_size
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135 --finetuning_samples $finetuning_samples
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136 --variance_threshold $variance_threshold
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137 --correlation_threshold $correlation_threshold
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138 --subsample $subsample
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139 --features_min $features_min
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140 --features_top_percentile $features_top_percentile
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141 --data_types $str(",".join($data_names))
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142 --early_stop_patience $early_stop_patience
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143 --hpo_patience $hpo_patience
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144 $log_transform
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145 $use_loss_weighting
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146 $use_cv
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147 $evaluate_baseline_performance
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148 --feature_importance_method $feature_importance_method
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149 \${GALAXY_FLEXYNESIS_EXTRA_ARGUMENTS}
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150
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151 ## convert flexynesis output files to tabular format
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152 && for file in output/*.csv; do
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153 if [ -f "\$file" ]; then
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154 basename="\${file%.csv}";
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155 python '$__tool_directory__/convert.py' "\$file" "\${basename}.tabular";
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156 echo "Converted \$file to \${basename}.tabular";
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157 fi
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158 done
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159 #if str($training_type.model) == 's_train':
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160 #if str($plot.plot_embeddings_conditional.plot_embeddings) == 'yes':
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161 && python '$__tool_directory__/flexynesis_plot.py'
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162 --plot_type dimred
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163 --embeddings output/job.embeddings_test.tabular
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164 --labels output/job.predicted_labels.tabular
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165 --method $plot.plot_embeddings_conditional.method
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166 #if str($training_type.model) == 's_train':
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167 #if str($target_variables) != 'None':
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168 --target_value \$targets
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169 #end if
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170 #end if
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171 --output_dir plots
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172 --format $plot.plot_embeddings_conditional.format
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173 --dpi $plot.plot_embeddings_conditional.dpi
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174 #end if
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175 #if str($plot.plot_km_conditional.plot_km) == 'yes':
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176 #if str($surv_event_var) == '' or str($surv_time_var) == '':
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177 && echo "Survival event and time variables must be specified for Kaplan-Meier plots."
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178 && exit 1
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179 #else
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180 && python '$__tool_directory__/flexynesis_plot.py'
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181 --plot_type kaplan_meier
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182 --labels output/job.predicted_labels.tabular
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183 --survival_data input/test/clin.csv
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184 --surv_event_var \$survival_event
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185 --surv_time_var \$survival_time
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186 --output_dir plots
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187 --format $plot.plot_km_conditional.format
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188 --dpi $plot.plot_km_conditional.dpi
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189 #end if
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190 #end if
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191 #if str($plot.plot_cox_conditional.plot_cox) == 'yes':
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192 #if str($surv_event_var) == '' or str($surv_time_var) == '':
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193 && echo "Survival event and time variables must be specified for cox plots."
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194 && exit 1
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195 #else
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196 && python '$__tool_directory__/flexynesis_plot.py'
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197 --plot_type cox
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198 #if str($feature_importance_method) == 'GradientShap':
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199 --important_features output/job.feature_importance.GradientShap.tabular
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200 #else if str($feature_importance_method) == 'IntegratedGradients':
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201 --important_features output/job.feature_importance.IntegratedGradients.tabular
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202 #else
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203 --important_features output/job.feature_importance.IntegratedGradients.tabular
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204 #end if
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205 --clinical_train input/train/clin.csv
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206 --clinical_test input/test/clin.csv
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207 #if str($plot.plot_cox_conditional.omics_name) != '':
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208 #set $omics_name = str($plot.plot_cox_conditional.omics_name.replace(" ", "_"))
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209 --omics_train input/train/${omics_name}.csv
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210 --omics_test input/test/${omics_name}.csv
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211 --layer ${omics_name}
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212 #else
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213 --omics_train input/train/${data_names}.csv
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214 --omics_test input/test/${data_names}.csv
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215 --layer ${data_names}
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216 #end if
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217 --surv_time_var \$survival_time
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218 --surv_event_var \$survival_event
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219 #if str($plot.plot_cox_conditional.clinical_variables) != 'None':
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220 --clinical_variables \$covars
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221 #end if
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222 --top_features $plot.plot_cox_conditional.top_features
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223 #if str($plot.plot_cox_conditional.crossval_conditional.crossval) == 'yes':
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224 --crossval
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225 #end if
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226 #if str($plot.plot_cox_conditional.crossval_conditional.crossval) == 'yes':
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227 --n_splits $plot.plot_cox_conditional.crossval_conditional.n_splits
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228 #end if
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229 --random_state 42
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230 --output_dir plots
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231 --format $plot.plot_cox_conditional.format
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232 --dpi $plot.plot_cox_conditional.dpi
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233 #end if
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234 #end if
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235 #if str($plot.plot_scatter_conditional.plot_scatter) == 'yes':
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236 && python '$__tool_directory__/flexynesis_plot.py'
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237 --plot_type scatter
5
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238 --labels output/job.predicted_labels.tabular
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239 #if str($training_type.model) == 's_train':
6
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240 #if str($target_variables) != 'None':
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241 --target_value \$targets
5
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242 #end if
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243 #end if
3
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244 --output_dir plots
6
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245 --format $plot.plot_scatter_conditional.format
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246 --dpi $plot.plot_scatter_conditional.dpi
3
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247 #end if
6
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248 #if str($plot.plot_concordance_conditional.plot_concordance) == 'yes':
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249 && python '$__tool_directory__/flexynesis_plot.py'
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250 --plot_type concordance_heatmap
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251 --labels output/job.predicted_labels.tabular
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252 #if str($training_type.model) == 's_train':
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253 #if str($target_variables) != 'None':
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254 --target_value \$targets
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255 #end if
0
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256 #end if
3
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257 --output_dir plots
6
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258 --format $plot.plot_concordance_conditional.format
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259 --dpi $plot.plot_concordance_conditional.dpi
3
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260 #end if
6
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261 #if str($plot.plot_pr_curves_conditional.plot_pr_curves) == 'yes':
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262 && python '$__tool_directory__/flexynesis_plot.py'
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263 --plot_type pr_curve
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264 --labels output/job.predicted_labels.tabular
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265 #if str($training_type.model) == 's_train':
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266 #if str($target_variables) != 'None':
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267 --target_value \$targets
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268 #end if
5
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269 #end if
6
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270 --output_dir plots
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271 --format $plot.plot_pr_curves_conditional.format
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272 --dpi $plot.plot_pr_curves_conditional.dpi
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273 #end if
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274 #if str($plot.plot_roc_curves_conditional.plot_roc_curves) == 'yes':
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275 && python '$__tool_directory__/flexynesis_plot.py'
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276 --plot_type roc_curve
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277 --labels output/job.predicted_labels.tabular
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278 #if str($training_type.model) == 's_train':
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279 #if str($target_variables) != 'None':
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280 --target_value \$targets
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281 #end if
5
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282 #end if
6
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283 --output_dir plots
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284 --format $plot.plot_roc_curves_conditional.format
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285 --dpi $plot.plot_roc_curves_conditional.dpi
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286 #end if
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287 #if str($plot.plot_boxplot_conditional.plot_boxplot) == 'yes':
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288 && python '$__tool_directory__/flexynesis_plot.py'
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289 --plot_type box_plot
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290 --labels output/job.predicted_labels.tabular
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291 #if str($training_type.model) == 's_train':
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292 #if str($target_variables) != 'None':
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293 --target_value \$targets
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294 #end if
5
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295 #end if
6
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296 --output_dir plots
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297 --format $plot.plot_boxplot_conditional.format
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298 --dpi $plot.plot_boxplot_conditional.dpi
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299 #end if
3
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300 #end if
0
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301 ]]></command>
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302 <inputs>
3
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303 <expand macro="commercial_use_param"/>
0
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304 <conditional name="training_type">
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305 <param name="model" type="select" label="Type of Analysis" >
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306 <option value="s_train">Supervised training</option>
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307 <option value="us_train">Unsupervised Training</option>
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308 <option value="cm_train">Cross-modality Training</option>
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309 </param>
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310 <when value="s_train">
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311 <expand macro="main_inputs"/>
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312 <repeat name="omics" min="0" title="Multiple omics layers?">
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313 <expand macro="extra_inputs"/>
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314 </repeat>
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315 <conditional name="model_class" label="Model class">
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316 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
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317 <option value="DirectPred">DirectPred</option>
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318 <option value="GNN">GNN</option>
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319 <option value="MultiTripletNetwork">MultiTripletNetwork</option>
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320 <option value="RandomForest">RandomForest</option>
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321 <option value="SVM">SVM</option>
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322 <option value="RandomSurvivalForest">RandomSurvivalForest</option>
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323 <option value="XGBoost">XGBoost</option>
0
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324 </param>
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325 <when value="DirectPred"/>
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326 <when value="GNN">
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327 <param argument="--gnn_conv_type" type="select" label="Which graph convolution type to use.">
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328 <option value="GC">GC</option>
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329 <option value="GCN">GCN</option>
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330 <option value="SAGE">SAGE</option>
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331 </param>
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332 <param argument="--string_organism" type="select" label="STRING DB organism">
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333 <option value="9606">Homo sapiens</option>
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334 <option value="10090">Mus musculus</option>
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335 <option value="10116">Rattus norvegicus</option>
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336 <option value="9544">Macaca mulatta</option>
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337 </param>
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338 <param argument="--string_node_name" type="select" label="String node name" >
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339 <option value="gene_name">Gene name</option>
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340 <option value="gene_id">Gene id</option>
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341 </param>
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342 </when>
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343 <when value="MultiTripletNetwork"/>
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344 <when value="RandomForest"/>
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345 <when value="SVM"/>
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346 <when value="RandomSurvivalForest"/>
1
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347 <when value="XGBoost"/>
0
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348 </conditional>
6
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349 <param argument="--target_variables" type="data_column" data_ref="train_clin" optional="true" multiple="true" label="Column name in the train clinical data to use for predictions, multiple targets are allowed"/>
5
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350 <param argument="--surv_event_var" type="data_column" data_ref="train_clin" optional="true" label="Column name in the train clinical data to use as survival event"/>
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351 <param argument="--surv_time_var" type="data_column" data_ref="train_clin" optional="true" label="Column name in the train clinical data to use as survival time"/>
0
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352 <expand macro="advanced"/>
6
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353 <section name="plot" title="Visualization">
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354 <conditional name="plot_embeddings_conditional">
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355 <param name="plot_embeddings" type="select" label="Generate embeddings plot?" help="Generate PCA or UMAP plot of the test dataset">
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diff changeset
356 <option value="yes">Yes</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
357 <option value="no" selected="true">No</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
358 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
359 <when value="no">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
360 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
361 <when value="yes">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
362 <param name="method" type="select" label="Transformation method">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
363 <option value="pca" selected="true">PCA</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
364 <option value="umap">UMAP</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
365 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
366 <expand macro="plots_common_param"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
367 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
368 </conditional>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
369 <conditional name="plot_km_conditional">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
370 <param name="plot_km" type="select" label="Generate kaplan meier curves plot?" help="Generate KM curves plot of risk subtype based on predicted events probabilities">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
371 <option value="yes">Yes</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
372 <option value="no" selected="true">No</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
373 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
374 <when value="no">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
375 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
376 <when value="yes">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
377 <expand macro="plots_common_param"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
378 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
379 </conditional>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
380 <conditional name="plot_cox_conditional">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
381 <param name="plot_cox" type="select" label="Generate hazard ratio plot?" help="Performs Cox regression on data based on top features and selected clinical covariates.">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
382 <option value="yes">Yes</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
383 <option value="no" selected="true">No</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
384 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
385 <when value="no">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
386 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
387 <when value="yes">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
388 <param name="omics_name" type="text" label="Omics layer to use for cox input" optional="true" help="If not specified, the first omics layer will be used.">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
389 <expand macro="sanitizer_printable"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
390 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
391 <param argument="--clinical_variables" type="data_column" data_ref="train_clin" optional="true" multiple="true" label="Columns in the train clinical data to use as clinical covariates and include in the Cox model (e.g SEX, AGE, ...), multiple covariates are allowed"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
392 <param argument="--top_features" type="integer" min="1" value="20" label="Number of top important features to include in Cox model"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
393 <conditional name="crossval_conditional">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
394 <param name="crossval" type="select" label="Performs K-fold cross-validation?">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
395 <option value="yes">Yes</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
396 <option value="no" selected="true">No</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
397 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
398 <when value="yes">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
399 <param name="n_splits" type="integer" min="2" value="5" label="Number of folds for cross-validation"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
400 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
401 <when value="no"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
402 </conditional>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
403 <expand macro="plots_common_param"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
404 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
405 </conditional>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
406 <conditional name="plot_scatter_conditional">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
407 <param name="plot_scatter" type="select" label="Generate scatter plot?" help="Generates a scatter plot of numeric true and predicted labels for all available targets.">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
408 <option value="yes">Yes</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
409 <option value="no" selected="true">No</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
410 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
411 <when value="no">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
412 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
413 <when value="yes">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
414 <expand macro="plots_common_param"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
415 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
416 </conditional>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
417 <conditional name="plot_concordance_conditional">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
418 <param name="plot_concordance" type="select" label="Generate concordance heatmap plot?" help="Generates a plot showing the concordance between true and predicted labels for all targets.">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
419 <option value="yes">Yes</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
420 <option value="no" selected="true">No</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
421 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
422 <when value="no">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
423 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
424 <when value="yes">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
425 <expand macro="plots_common_param"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
426 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
427 </conditional>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
428 <conditional name="plot_pr_curves_conditional">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
429 <param name="plot_pr_curves" type="select" label="Generate precision-recall curves plot?" help="Generates precision-recall curves for all available targets.">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
430 <option value="yes">Yes</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
431 <option value="no" selected="true">No</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
432 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
433 <when value="no">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
434 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
435 <when value="yes">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
436 <expand macro="plots_common_param"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
437 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
438 </conditional>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
439 <conditional name="plot_roc_curves_conditional">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
440 <param name="plot_roc_curves" type="select" label="Generate ROC curves plot?" help="Generates ROC curves for all available targets.">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
441 <option value="yes">Yes</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
442 <option value="no" selected="true">No</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
443 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
444 <when value="no">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
445 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
446 <when value="yes">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
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diff changeset
447 <expand macro="plots_common_param"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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448 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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449 </conditional>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
450 <conditional name="plot_boxplot_conditional">
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451 <param name="plot_boxplot" type="select" label="Generate boxplot?" help="Generates a boxplot for all available targets.">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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452 <option value="yes">Yes</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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453 <option value="no" selected="true">No</option>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
454 </param>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
455 <when value="no">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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456 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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457 <when value="yes">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
458 <expand macro="plots_common_param"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
459 </when>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
460 </conditional>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
461 </section>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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462 </when>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
463 <when value="us_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
464 <expand macro="main_inputs"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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465 <repeat name="omics" min="0" title="Multiple omics layers?">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
466 <expand macro="extra_inputs"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
467 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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468 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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469 <option value="supervised_vae">supervised_vae</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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470 </param>
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diff changeset
471 <expand macro="advanced"/>
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472 </when>
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473 <when value="cm_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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474 <expand macro="main_inputs"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
475 <param name="layer_main" type="select" label="Use this omics data as input or output layer?">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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476 <option value="input">Input</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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477 <option value="output">output</option>
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478 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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479 <repeat name="omics" min="0" title="Multiple omics layers?">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
480 <expand macro="extra_inputs"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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481 <param name="layer" type="select" label="Use this omics data as input or output layer?">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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482 <option value="input">Input</option>
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483 <option value="output">output</option>
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484 </param>
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diff changeset
485 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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486 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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487 <option value="CrossModalPred">CrossModalPred</option>
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488 </param>
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diff changeset
489 <expand macro="advanced"/>
3
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490 </when>
0
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491 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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492 </inputs>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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493 <outputs>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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494 <collection name="results" type="list" label="${tool.name} on ${on_string}: results">
5
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diff changeset
495 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tabular$" format="tabular" directory="output"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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496 </collection>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
497 <collection name="plots" type="list" label="${tool.name} on ${on_string}: plots">
3
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diff changeset
498 <discover_datasets pattern="__name_and_ext__" directory="plots"/>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
499 <filter>training_type['model'] == 's_train' and (training_type['plot']['plot_embeddings_conditional']['plot_embeddings'] == 'yes' or training_type['plot']['plot_km_conditional']['plot_km'] == 'yes' or training_type['plot']['plot_cox_conditional']['plot_cox'] == 'yes' or training_type['plot']['plot_scatter_conditional']['plot_scatter'] == 'yes' or training_type['plot']['plot_concordance_conditional']['plot_concordance'] == 'yes' or training_type['plot']['plot_pr_curves_conditional']['plot_pr_curves'] == 'yes' or training_type['plot']['plot_roc_curves_conditional']['plot_roc_curves'] == 'yes' or training_type['plot']['plot_boxplot_conditional']['plot_boxplot'] == 'yes')</filter>
3
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diff changeset
500 </collection>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
501 </outputs>
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diff changeset
502 <tests>
3
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503 <!-- test 1: Supervised training with GEX and CNV data, DirectPred model, Erlotinib target -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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504 <test expect_num_outputs="1">
0
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505 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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506 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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507 <param name="model" value="s_train"/>
5
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diff changeset
508 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
509 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
510 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
511 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
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diff changeset
512 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
513 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
514 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
515 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
516 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
517 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
518 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
519 <param name="model_class" value="DirectPred"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
520 </conditional>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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diff changeset
521 <param name="target_variables" value="3"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
522 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
523 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
524 </section>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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525 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
526 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
527 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
528 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
529 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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530 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
531 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
532 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
533 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
534 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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535 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
536 </element>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
537 <element name="job.feature_importance.GradientShap">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
538 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
539 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
540 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
541 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
542 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
543 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
544 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
545 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
546 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
547 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
548 <has_text_matching expression="IntegratedGradients"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
549 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
550 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
551 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
552 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
553 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
554 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
555 </element>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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parents: 5
diff changeset
556 <element name="job.feature_logs.foo">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
557 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
558 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
559 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
560 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
561 <element name="job.predicted_labels">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
562 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
563 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
564 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
565 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
566 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
567 <element name="job.stats">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
568 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
569 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
570 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
571 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
572 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
573 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
574 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
575 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
576 <!-- test 2: Supervised training with GEX data, DirectPred model, Erlotinib target -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
577 <test expect_num_outputs="1">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
578 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
579 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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580 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
581 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
582 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
583 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
584 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
585 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
586 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
587 <param name="model_class" value="DirectPred"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
588 </conditional>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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parents: 5
diff changeset
589 <param name="target_variables" value="3"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
590 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
591 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
592 </section>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
593 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
594 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
595 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
596 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
597 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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598 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
599 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
600 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
601 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
602 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
603 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
604 </element>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
605 <element name="job.feature_importance.GradientShap">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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606 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
607 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
608 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
609 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
610 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
611 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
612 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
613 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
614 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
615 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
616 <has_text_matching expression="IntegratedGradients"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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617 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
618 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
619 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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620 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
621 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
622 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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623 </element>
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624 <element name="job.predicted_labels">
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625 <assert_contents>
5
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626 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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627 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
0
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628 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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629 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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630 <element name="job.stats">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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631 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
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632 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
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633 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
634 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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635 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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636 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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637 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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638 </test>
3
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parents: 1
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639 <!-- test 3: Supervised training with GEX and CNV data, DirectPred model, Irinotecan target -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
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640 <test expect_num_outputs="1">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
641 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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642 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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643 <param name="model" value="s_train"/>
5
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diff changeset
644 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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645 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
646 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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647 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
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parents: 0
diff changeset
648 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
649 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
650 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
651 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
652 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
653 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
654 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
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655 <param name="model_class" value="DirectPred"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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656 </conditional>
6
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diff changeset
657 <param name="target_variables" value="4"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
658 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
659 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
660 </section>
0
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661 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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662 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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663 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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664 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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665 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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666 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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667 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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668 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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669 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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670 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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671 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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672 </element>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
673 <element name="job.feature_importance.GradientShap">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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674 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
675 <has_text_matching expression="Irinotecan\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
676 <has_text_matching expression="Irinotecan\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
677 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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678 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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679 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
680 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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681 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
682 <has_text_matching expression="Irinotecan\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
683 <has_text_matching expression="Irinotecan\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
684 <has_text_matching expression="IntegratedGradients"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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685 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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686 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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687 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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688 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
689 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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690 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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691 </element>
6
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diff changeset
692 <element name="job.feature_logs.foo">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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693 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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694 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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695 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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696 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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697 <element name="job.predicted_labels">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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698 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
699 <has_text_matching expression="source_dataset:A-704\tIrinotecan\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
700 <has_text_matching expression="target_dataset:KMRC-20\tIrinotecan\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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701 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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702 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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703 <element name="job.stats">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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704 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
705 <has_text_matching expression="DirectPred\tIrinotecan\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
706 <has_text_matching expression="DirectPred\tIrinotecan\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
707 <has_text_matching expression="DirectPred\tIrinotecan\tnumerical\tpearson_corr\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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708 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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709 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
710 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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711 </test>
3
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diff changeset
712 <!-- test 4: Un-supervised training with GEX and CNV data, supervised_vae model -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
713 <test expect_num_outputs="1">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
714 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
715 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
716 <param name="model" value="us_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
717 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
718 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
719 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
720 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
721 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
722 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
723 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
724 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
725 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
726 </repeat>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
727 <param name="model_class" value="supervised_vae"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
728 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
729 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
730 </section>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
731 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
732 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
733 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
734 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
735 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
736 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
737 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
738 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
739 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
740 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
741 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
742 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
743 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
744 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
745 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
746 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
747 </element>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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parents: 5
diff changeset
748 <element name="job.feature_logs.foo">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
749 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
750 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
751 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
752 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
753 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
754 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
755 <!-- test 5: Cross-modality training with GEX and CNV data, CrossModalPred model -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
756 <test expect_num_outputs="1">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
757 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
758 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
759 <param name="model" value="cm_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
760 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
761 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
762 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
763 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
764 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
765 <param name="layer_main" value="input"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
766 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
767 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
768 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
769 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
770 <param name="layer" value="output"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
771 </repeat>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
772 <param name="model_class" value="CrossModalPred"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
773 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
774 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
775 </section>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
776 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
777 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
778 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
779 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
780 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
781 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
782 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
783 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
784 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
785 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
786 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
787 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
788 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
789 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
790 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
791 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
792 </element>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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parents: 5
diff changeset
793 <element name="job.feature_logs.foo">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
794 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
795 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
796 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
797 </element>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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parents: 5
diff changeset
798 <element name="job.test_decoded.foo">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
799 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
800 <has_n_lines n="23"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
801 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
802 </element>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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parents: 5
diff changeset
803 <element name="job.train_decoded.foo">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
804 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
805 <has_n_lines n="23"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
806 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
807 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
808 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
809 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
810 <!-- test 6: Supervised training with GEX and CNV data, GNN model, Erlotinib target -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
811 <test expect_num_outputs="1">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
812 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
813 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
814 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
815 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
816 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
817 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
818 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
819 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
820 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
821 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
822 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
823 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
824 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
825 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
826 <param name="model_class" value="GNN"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
827 <param name="gnn_conv_type" value="GC"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
828 <param name="string_organism" value="9606"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
829 <param name="string_node_name" value="gene_name"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
830 </conditional>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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parents: 5
diff changeset
831 <param name="target_variables" value="3"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
832 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
833 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
834 </section>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
835 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
836 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
837 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
838 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
839 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
840 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
841 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
842 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
843 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
844 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
845 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
846 </element>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
847 <element name="job.feature_importance.GradientShap">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
848 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
849 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
850 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
851 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
852 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
853 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
854 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
855 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
856 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
857 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
858 <has_text_matching expression="IntegratedGradients"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
859 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
860 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
861 <element name="job.feature_logs.bar">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
862 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
863 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
864 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
865 </element>
6
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parents: 5
diff changeset
866 <element name="job.feature_logs.foo">
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
867 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
868 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
869 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
870 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
871 <element name="job.predicted_labels">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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872 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
873 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
874 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
1
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diff changeset
875 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
876 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
877 <element name="job.stats">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
878 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
879 <has_text_matching expression="GNN\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
880 <has_text_matching expression="GNN\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
881 <has_text_matching expression="GNN\tErlotinib\tnumerical\tpearson_corr\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
882 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
883 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
884 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
885 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
886 <!-- test 7: test 4 + checking whitespace in assay name -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
887 <test expect_num_outputs="1">
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
888 <param name="non_commercial_use" value="True"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
889 <conditional name="training_type">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
890 <param name="model" value="us_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
891 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
892 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
893 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
894 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
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bgruening
parents: 0
diff changeset
895 <param name="assay_main" value="b ar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
896 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
897 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
898 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
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bgruening
parents: 0
diff changeset
899 <param name="assay" value="f oo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
900 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
901 <param name="model_class" value="supervised_vae"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
902 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
903 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
904 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
905 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
906 <output_collection name="results" type="list">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
907 <element name="job.embeddings_test">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
908 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
909 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
910 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
911 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
912 <element name="job.embeddings_train">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
913 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
914 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
915 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
916 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
917 <element name="job.feature_logs.b_ar">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
918 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
919 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
920 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
921 </element>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
922 <element name="job.feature_logs.f_oo">
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
923 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
924 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
925 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
926 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
927 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
928 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
929 <!-- test 8: Supervised training with GEX and CNV data, XGBoost model, Erlotinib target -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
930 <test expect_num_outputs="1">
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
931 <param name="non_commercial_use" value="True"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
932 <conditional name="training_type">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
933 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
934 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
935 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
936 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
937 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
938 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
939 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
940 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
941 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
942 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
943 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
944 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
945 <param name="model_class" value="XGBoost"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
946 </conditional>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
947 <param name="target_variables" value="3"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
948 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
949 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
950 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
951 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
952 <output_collection name="results" type="list">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
953 <element name="job.stats">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
954 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
955 <has_text_matching expression="XGBoostRegressor\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
956 <has_text_matching expression="XGBoostRegressor\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
957 <has_text_matching expression="XGBoostRegressor\tErlotinib\tnumerical\tpearson_corr\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
958 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
959 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
960 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
961 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
962 <!-- test 9: test 1 + checking IntegratedGradients method -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
963 <test expect_num_outputs="1">
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
964 <param name="non_commercial_use" value="True"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
965 <conditional name="training_type">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
966 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
967 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
968 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
969 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
970 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
971 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
972 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
973 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
974 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
975 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
976 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
977 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
978 <param name="model_class" value="DirectPred"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
979 </conditional>
6
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diff changeset
980 <param name="target_variables" value="3"/>
1
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parents: 0
diff changeset
981 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
982 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
983 <param name="feature_importance_method" value="IntegratedGradients"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
984 <param name="val_size" value="0.2"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
985 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
986 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
987 <output_collection name="results" type="list">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
988 <element name="job.embeddings_test">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
989 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
990 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
991 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
992 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
993 <element name="job.embeddings_train">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
994 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
995 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
996 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
997 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
998 <element name="job.feature_importance.IntegratedGradients">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
999 <assert_contents>
5
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parents: 4
diff changeset
1000 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
1001 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1002 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1003 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1004 <element name="job.feature_logs.bar">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1005 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1006 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1007 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1008 </element>
6
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parents: 5
diff changeset
1009 <element name="job.feature_logs.foo">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1010 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1011 <has_n_lines n="25"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1012 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1013 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1014 <element name="job.predicted_labels">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1015 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1016 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1017 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1018 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1019 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1020 <element name="job.stats">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1021 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1022 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1023 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1024 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1025 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1026 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1027 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1028 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1029 <!-- test 10: dimred plot -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1030 <test expect_num_outputs="2">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1031 <param name="non_commercial_use" value="True"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1032 <conditional name="training_type">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1033 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1034 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1035 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1036 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1037 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1038 <param name="assay_main" value="bar"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1039 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1040 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1041 <param name="test_omics" value="test/cnv" ftype="tabular"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1042 <param name="assay" value="foo"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1043 </repeat>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1044 <conditional name="model_class">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1045 <param name="model_class" value="DirectPred"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1046 </conditional>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1047 <param name="target_variables" value="3"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1048 <section name="advanced">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1049 <param name="hpo_iter" value="1"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1050 </section>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1051 <section name="plot">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1052 <conditional name="plot_embeddings_conditional">
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1053 <param name="plot_embeddings" value="yes"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1054 <param name="method" value="pca"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1055 <param name="format" value="jpg"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1056 <param name="dpi" value="300"/>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1057 </conditional>
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1058 </section>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1059 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1060 <output_collection name="results" type="list">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1061 <element name="job.embeddings_test">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1062 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1063 <has_n_lines n="50"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1064 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1065 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1066 <element name="job.embeddings_train">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1067 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1068 <has_n_lines n="50"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1069 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1070 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1071 <element name="job.feature_importance.GradientShap">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1072 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1073 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1074 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1075 <has_text_matching expression="GradientShap"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1076 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1077 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1078 <element name="job.feature_importance.IntegratedGradients">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1079 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1080 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1081 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1082 <has_text_matching expression="IntegratedGradients"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1083 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1084 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1085 <element name="job.feature_logs.bar">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1086 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1087 <has_n_lines n="25"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1088 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1089 </element>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1090 <element name="job.feature_logs.foo">
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1091 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1092 <has_n_lines n="25"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1093 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1094 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1095 <element name="job.predicted_labels">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1096 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1097 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1098 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1099 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1100 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1101 <element name="job.stats">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1102 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1103 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1104 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1105 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1106 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1107 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1108 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1109 <output_collection name="plots" type="list">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1110 <element name="job.embeddings_test_pca_Erlotinib_known">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1111 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1112 <has_image_center_of_mass center_of_mass="962,732" eps="20"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1113 <has_image_channels channels="3"/>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1114 <has_image_height height="1461" delta="10"/>
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1115 <has_image_width width="1941" delta="10"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1116 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1117 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1118 <element name="job.embeddings_test_pca_Erlotinib_predicted">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1119 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1120 <has_image_center_of_mass center_of_mass="959.5,732.5" eps="20"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1121 <has_image_channels channels="3"/>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1122 <has_image_height height="1461" delta="10"/>
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1123 <has_image_width width="1941" delta="10"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1124 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1125 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1126 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1127 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1128 <!-- test 11: km plot -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1129 <test expect_num_outputs="2">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1130 <expand macro="common_test">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1131 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1132 <conditional name="plot_km_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1133 <param name="plot_km" value="yes"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1134 <param name="format" value="jpg"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1135 <param name="dpi" value="300"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1136 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1137 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1138 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1139 <output_collection name="plots" type="list">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1140 <element name="clin_km_km_risk_subtypes">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1141 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1142 <has_image_center_of_mass center_of_mass="971,732" eps="20"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1143 <has_image_channels channels="3"/>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1144 <has_image_height height="1461" delta="10"/>
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1145 <has_image_width width="1941" delta="10"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1146 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1147 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1148 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1149 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1150 <!-- test 12: cox plot -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1151 <test expect_num_outputs="2">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1152 <expand macro="common_test">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1153 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1154 <conditional name="plot_cox_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1155 <param name="plot_cox" value="yes"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1156 <param name="omics_name" value="bar"/>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1157 <param name="clinical_variables" value="2,3"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1158 <param name="top_features" value="10"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1159 <param name="format" value="jpg"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1160 <param name="dpi" value="300"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1161 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1162 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1163 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1164 <output_collection name="plots" type="list">
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1165 <element name="job.feature_importance.IntegratedGradients_cox_hazard_ratios">
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1166 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1167 <has_image_center_of_mass center_of_mass="972,737" eps="20"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1168 <has_image_channels channels="3"/>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1169 <has_image_height height="1461" delta="10"/>
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1170 <has_image_width width="1941" delta="10"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1171 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1172 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1173 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1174 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1175 <!-- test 13: scatter plot -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1176 <test expect_num_outputs="2">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1177 <expand macro="common_test">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1178 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1179 <conditional name="plot_scatter_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1180 <param name="plot_scatter" value="yes"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1181 <param name="format" value="jpg"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1182 <param name="dpi" value="300"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1183 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1184 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1185 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1186 <output_collection name="plots" type="list">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1187 <element name="job.predicted_labels_scatter_Erlotinib">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1188 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1189 <has_image_center_of_mass center_of_mass="969,735" eps="20"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1190 <has_image_channels channels="3"/>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1191 <has_image_height height="1461" delta="10"/>
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1192 <has_image_width width="1940" delta="10"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1193 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1194 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1195 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1196 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1197 <!-- test 14: concordance plot -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1198 <test expect_num_outputs="2">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1199 <expand macro="common_test">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1200 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1201 <conditional name="plot_concordance_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1202 <param name="plot_concordance" value="yes"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1203 <param name="format" value="jpg"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1204 <param name="dpi" value="300"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1205 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1206 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1207 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1208 <output_collection name="plots" type="list">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1209 <element name="job.predicted_labels_concordance_Erlotinib">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1210 <assert_contents>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1211 <has_image_center_of_mass center_of_mass="1547,1590" eps="30"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1212 <has_image_channels channels="3"/>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1213 <has_image_height height="3000" delta="50"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1214 <has_image_width width="3192" delta="50"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1215 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1216 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1217 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1218 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1219 <!-- test 15: pr curve plot -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1220 <test expect_num_outputs="2">
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1221 <expand macro="common_test_class">
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1222 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1223 <conditional name="plot_pr_curves_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1224 <param name="plot_pr_curves" value="yes"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1225 <param name="format" value="jpg"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1226 <param name="dpi" value="300"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1227 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1228 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1229 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1230 <output_collection name="plots" type="list">
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1231 <element name="job.predicted_labels_pr_curves_class">
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1232 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1233 <has_image_center_of_mass center_of_mass="975,732" eps="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1234 <has_image_channels channels="3"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1235 <has_image_height height="1461" delta="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1236 <has_image_width width="1941" delta="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1237 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1238 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1239 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1240 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1241 <!-- test 16: roc curve plot -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1242 <test expect_num_outputs="2">
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1243 <expand macro="common_test_class">
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1244 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1245 <conditional name="plot_roc_curves_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1246 <param name="plot_roc_curves" value="yes"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1247 <param name="format" value="jpg"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1248 <param name="dpi" value="300"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1249 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1250 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1251 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1252 <output_collection name="plots" type="list">
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1253 <element name="job.predicted_labels_roc_curves_class">
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1254 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1255 <has_image_center_of_mass center_of_mass="970,730" eps="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1256 <has_image_channels channels="3"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1257 <has_image_height height="1461" delta="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1258 <has_image_width width="1941" delta="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1259 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1260 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1261 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1262 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1263 <!-- test 17: boxplot plot -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1264 <test expect_num_outputs="2">
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1265 <expand macro="common_test_class">
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1266 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1267 <conditional name="plot_boxplot_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1268 <param name="plot_boxplot" value="yes"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1269 <param name="format" value="jpg"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1270 <param name="dpi" value="300"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1271 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1272 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1273 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1274 <output_collection name="plots" type="list">
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1275 <element name="job.predicted_labels_box_plot_class_buz">
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1276 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1277 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1278 <has_image_channels channels="3"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1279 <has_image_height height="1783" delta="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1280 <has_image_width width="2967" delta="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1281 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1282 </element>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1283 <element name="job.predicted_labels_box_plot_class_qux">
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1284 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1285 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1286 <has_image_channels channels="3"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1287 <has_image_height height="1765" delta="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1288 <has_image_width width="2967" delta="20"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1289 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1290 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1291 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1292 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1293 <!-- test 18: cox plot with multiple clinical variables + crossvar-->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1294 <test expect_num_outputs="2">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1295 <expand macro="common_test">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1296 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1297 <conditional name="plot_cox_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1298 <param name="plot_cox" value="yes"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1299 <param name="omics_name" value="bar"/>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1300 <param name="clinical_variables" value="2,3"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1301 <param name="top_features" value="10"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1302 <conditional name="crossval_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1303 <param name="crossval" value="yes"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1304 <param name="n_splits" value="5"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1305 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1306 <param name="format" value="jpg"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1307 <param name="dpi" value="300"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1308 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1309 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1310 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1311 <output_collection name="plots" type="list">
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1312 <element name="job.feature_importance.IntegratedGradients_cox_hazard_ratios">
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1313 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1314 <has_image_center_of_mass center_of_mass="972,737" eps="20"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1315 <has_image_channels channels="3"/>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1316 <has_image_height height="1461" delta="10"/>
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1317 <has_image_width width="1941" delta="10"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1318 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1319 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1320 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1321 </test>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1322 <!-- test 19: Supervised training with GEX and CNV data, DirectPred model, Erlotinib and Crizotinib targets -->
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1323 <test expect_num_outputs="1">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1324 <param name="non_commercial_use" value="True"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1325 <conditional name="training_type">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1326 <param name="model" value="s_train"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1327 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1328 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1329 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1330 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1331 <param name="assay_main" value="bar"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1332 <repeat name="omics">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1333 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1334 <param name="test_omics" value="test/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1335 <param name="assay" value="foo"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1336 </repeat>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1337 <conditional name="model_class">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1338 <param name="model_class" value="DirectPred"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1339 </conditional>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1340 <param name="target_variables" value="3,2"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1341 <section name="advanced">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1342 <param name="hpo_iter" value="1"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1343 </section>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1344 </conditional>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1345 <assert_stdout>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1346 <has_text_matching expression="Target variables: Erlotinib,Crizotinib"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1347 </assert_stdout>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1348 <output_collection name="results" type="list">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1349 <element name="job.embeddings_test">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1350 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1351 <has_n_lines n="50"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1352 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1353 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1354 <element name="job.embeddings_train">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1355 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1356 <has_n_lines n="50"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1357 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1358 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1359 <element name="job.feature_importance.GradientShap">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1360 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1361 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1362 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1363 <has_text_matching expression="Crizotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1364 <has_text_matching expression="Crizotinib\t0\t\tbar\tABCC4\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1365 <has_text_matching expression="GradientShap"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1366 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1367 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1368 <element name="job.feature_importance.IntegratedGradients">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1369 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1370 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1371 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1372 <has_text_matching expression="Crizotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1373 <has_text_matching expression="Crizotinib\t0\t\tbar\tABCC4\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1374 <has_text_matching expression="IntegratedGradients"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1375 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1376 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1377 <element name="job.feature_logs.bar">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1378 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1379 <has_n_lines n="25"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1380 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1381 </element>
6
33816f44fc7d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 5
diff changeset
1382 <element name="job.feature_logs.foo">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1383 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1384 <has_n_lines n="25"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1385 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1386 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1387 <element name="job.predicted_labels">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1388 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1389 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1390 <has_text_matching expression="source_dataset:A-704\tCrizotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1391 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1392 <has_text_matching expression="target_dataset:KMRC-20\tCrizotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1393 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1394 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1395 <element name="job.stats">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1396 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1397 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1398 <has_text_matching expression="DirectPred\tCrizotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1399 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1400 <has_text_matching expression="DirectPred\tCrizotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1401 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1402 <has_text_matching expression="DirectPred\tCrizotinib\tnumerical\tpearson_corr\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1403 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1404 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1405 </output_collection>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1406 </test>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1407 </tests>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1408 <help><![CDATA[
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1409 @COMMON_HELP@
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1410
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1411 .. image:: https://raw.githubusercontent.com/BIMSBbioinfo/flexynesis/c4634d97f84e51f569dcfdab2caf42c9be453ef6/img/graphical_abstract.jpg
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1412 :width: 600
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1413
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1414 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1415
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1416 **Input Files**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1417
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1418 **clin.tabular**
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1419
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1420 clin.tabular contains the sample metadata. The first column contains unique sample identifiers. The other columns contain sample-associated clinical variables. NA values are allowed in the clinical variables.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1421
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1422 The format might look like so:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1423
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1424 ======== === === ===
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1425 , v1 v2 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1426 -------- --- --- ---
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1427 sample1 a b ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1428 -------- --- --- ---
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1429 sample2 c d ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1430 -------- --- --- ---
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
1431 sample3 e f ...
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1432 -------- --- --- ---
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1433 ... ... ... ...
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1434 ======== === === ===
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1435
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1436 .
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1437
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1438 **omics.tabular**
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1439
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
1440 The first column of the feature tables must be unique feature identifiers (e.g. gene names). The column names must be sample identifiers that should overlap with those in the clin.tabular. They don't have to be completely identical or in the same order. Samples from the clin.tabular that are not represented in the omics table will be dropped.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
1441
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1442 The format might look like so:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1443
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1444 ===== ======= ======= ======= =======
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1445 , sample1 sample2 sample3 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1446 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1447 gene1 0 1 2 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1448 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1449 gene2 3 3 5 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1450 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1451 gene3 2 3 4 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1452 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1453 ... ... ... ... ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1454 ===== ======= ======= ======= =======
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1455
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1456 .
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1457
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1458 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1459
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1460 **Concordance between train/test splits:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1461
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1462 The corresponding omics files in train/test splits must contain overlapping feature names (they don't have to be identical or in the same order). The clin.tabular files in train/test must contain matching clinical variables.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1463
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1464 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1465
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1466 **Supervised Training**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1467
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1468 **Minimum requirements**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1469
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
1470 * clin.tabular and omics.tabular files for training and testing
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
1471 * Selection of a tool/model
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1472 * One target variable which can be numerical or categorical for regression/classification tasks.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1473
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
1474 Flexynesis supports both single-task and multi-task training. We can provide one or more target variables and optionally survival variables as input and Flexynesis will build the appropriate model architecture. If the selected variable is numerical, a Multi-Layered-Perceptron (MLP) with MSE loss will be used. If a categorical variable is provided, an MLP with cross-entropy-loss will be utilized. If survival variables are provided, an MLP with Cox-Proportional-Hazards loss will be attached to the model.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
1475
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1476 **Regression:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1477
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1478
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1479 If your target variable is numerical, Flexynesis will build a regression model.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1480
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1481 **Classification:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1482
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1483
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1484 If your target variable is categorical, Flexynesis will build a classification model.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1485
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1486 **Survival Analysis:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1487
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1488
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1489 If your target variable is survival data, Flexynesis will build a survival analysis model.
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
1490 For survival analysis, two separate variables are required, where the first variable is a numeric event variable (consisting of 0's or 1's, where 1 means an event such as disease progression or death has occurred). The second variable is also a numeric time variable, which indicates how much time it took since last patient follow-up.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1491
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
1492 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1493
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
1494 **Note:** Flexynesis can be trained with multiple target variables, which can be a mixture of regression/classification/survival tasks.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1495
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
1496 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1497
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
1498 **Note:** For the supervised tasks, the user can easily switch between different model architectures.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1499
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1500 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1501
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1502 **Note:** If you choose **MultiTripletNetwork** model, the first target variable should be a categorical variable.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1503
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1504 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1505
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1506 **Note:** If you choose **GNN** model, the features should have the same naming convention between different omics modalities.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1507
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1508 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1509
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1510 **Note:** The **GNN** model only works with genes (for example CpG methylation sites does not work). The reason is that GNNs require a prior knowledge network, which is currently set to use STRING database.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1511
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1512 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1513
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1514 **Unsupervised Training**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1515
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
1516 In the absence of any target variables or survival variables, you can use a VAE architecture to carry out unsupervised training.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1517
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1518 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1519
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1520 **Cross-modality Training**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1521
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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1522 We have implemented a special case of VAEs where the input data layers and output data layers can be set to different data modalities. The purpose of a cross-modality encoder is to learn embeddings that can translate from one data modality to another. Crossmodality encoder we implemented supports both single/multiple input layers and also one or more target/survival variables can be added to the model.
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1523
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1524 .. class:: infomark
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1525
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1526 **Note:** if you use same input and output layers, it will be the same as unsupervised training.
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1527
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1528 -----
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1529
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1530 .. class:: infomark
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1531
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1532 **Modality fusion:**
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1533
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1534 Flexynesis currently supports two main ways of fusing different omics data modalities: 1. Early fusion: The input data matrices are initially concatenated and pushed through the networks 2. Intermediate fusion: The input data matrices are initially pushed through the networks to obtain a modality-specific embedding space, which then gets concatenated to serve as input for the supervisor MLPs.
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1535
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1536 .. _Documentation: https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/site/
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1537 .. _copyright holders: https://github.com/BIMSBbioinfo/flexynesis
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1538 ]]></help>
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1539 <expand macro="creator"/>
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1540 <expand macro="citations"/>
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1541 </tool>