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annotate flexynesis.xml @ 4:1a5f8cedda43 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
author bgruening
date Mon, 30 Jun 2025 17:19:10 +0000
parents 525c661a7fdc
children 466b593fd87e
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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 </required_files>
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11 <command detect_errors="exit_code"><![CDATA[
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12 @CHECK_NON_COMMERCIAL_USE@
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13 mkdir -p input/test input/train output &&
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14 ln -s '$train_clin' input/train/clin.csv &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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15 ln -s '$test_clin' input/test/clin.csv &&
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16
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17 #if str($assay_main) != '':
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18 #set $name = str($assay_main.replace(" ", "_"))
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19 ln -s '$train_omics_main' input/train/${name}.csv &&
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20 ln -s '$test_omics_main' input/test/${name}.csv &&
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21 #set $data_names = [$name]
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22 #else
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23 ln -s '$train_omics_main' input/train/main.csv &&
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24 ln -s '$test_omics_main' input/test/main.csv &&
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25 #set $data_names = ['main']
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26 #end if
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27 #if str($training_type.model) == 'cm_train':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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28 #if str($layer_main) == 'input':
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29 #set $input_layers = $data_names
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30 #set $output_layers = []
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31 #else
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32 #set $input_layers = []
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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33 #set $output_layers = $data_names
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34 #end if
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35 #end if
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36 #for $i, $element in enumerate($omics)
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37 #if str($element.train_omics) != 'None' and str($element.test_omics) != 'None':
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38 #if str($element.assay) != '':
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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39 #set $i = str($element.assay.replace(" ", "_"))
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40 #end if
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41 ln -s '${element.train_omics}' input/train/omics_${i}.csv &&
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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42 ln -s '${element.test_omics}' input/test/omics_${i}.csv &&
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43 $data_names.append("omics_" + str($i))
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44 #if str($training_type.model) == 'cm_train':
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45 #if str($element.layer) == 'input':
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46 $input_layers.append("omics_" + str($i))
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47 #else
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48 $output_layers.append("omics_" + str($i))
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49 #end if
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50 #end if
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51 #end if
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52 #end for
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53 flexynesis
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54 --data_path input
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55 --outdir output
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56 --model_class $model_class
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57 #if str($model_class) == 'GNN':
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58 --gnn_conv_type $gnn_conv_type
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59 --string_organism $string_organism
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60 --string_node_name $string_node_name
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61 #end if
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62 #if str($training_type.model) == 's_train':
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63 #if str($target_variables) != '':
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64 --target_variables $target_variables
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65 #end if
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66 #if str($surv_event_var) != '':
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67 --surv_event_var $surv_event_var
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68 --surv_time_var $surv_time_var
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69 #end if
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70 #end if
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71 #if str($training_type.model) == 'cm_train':
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72 --input_layers $str(",".join($input_layers))
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73 --output_layers $str(",".join($output_layers))
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74 #end if
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75 --fusion_type $fusion_type
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76 --hpo_iter $hpo_iter
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77 --val_size $val_size
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78 --finetuning_samples $finetuning_samples
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79 --variance_threshold $variance_threshold
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80 --correlation_threshold $correlation_threshold
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81 --subsample $subsample
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82 --features_min $features_min
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83 --features_top_percentile $features_top_percentile
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84 --data_types $str(",".join($data_names))
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85 --early_stop_patience $early_stop_patience
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86 --hpo_patience $hpo_patience
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87 $log_transform
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88 $use_loss_weighting
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89 $use_cv
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90 $evaluate_baseline_performance
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91 --feature_importance_method $feature_importance_method
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92 \${GALAXY_FLEXYNESIS_EXTRA_ARGUMENTS}
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93 #if str($plot.plot_embeddings_conditional.plot_embeddings) == 'yes':
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94 && python $__tool_directory__/flexynesis_plot.py
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95 --plot_type dimred
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96 --embeddings output/job.embeddings_test.csv
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97 --labels output/job.predicted_labels.csv
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98 --method $plot.plot_embeddings_conditional.method
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99 --target_variables $target_variables
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100 --output_dir plots
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101 --format $plot.plot_embeddings_conditional.format
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102 --dpi $plot.plot_embeddings_conditional.dpi
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103 #end if
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104 #if str($plot.plot_km_conditional.plot_km) == 'yes':
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105 #if str($surv_event_var) == '' or str($surv_time_var) == '':
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106 && echo "Survival event and time variables must be specified for Kaplan-Meier plots."
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107 && exit 1
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108 #else
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109 && python $__tool_directory__/flexynesis_plot.py
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110 --plot_type kaplan_meier
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111 --labels output/job.predicted_labels.csv
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112 --survival_data input/test/clin.csv
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113 --surv_event_var $surv_event_var
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114 --surv_time_var $surv_time_var
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115 --event_value $plot.plot_km_conditional.event_value
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116 --output_dir plots
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117 --format $plot.plot_km_conditional.format
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118 --dpi $plot.plot_km_conditional.dpi
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119 #end if
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120 #end if
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121 #if str($plot.plot_cox_conditional.plot_cox) == 'yes':
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122 #if str($surv_event_var) == '' or str($surv_time_var) == '':
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123 && echo "Survival event and time variables must be specified for cox plots."
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124 && exit 1
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125 #else
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126 && python $__tool_directory__/flexynesis_plot.py
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127 --plot_type cox
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128 --model output/job.final_model.pth
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129 --clinical_train input/train/clin.csv
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130 --clinical_test input/test/clin.csv
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131 #if str($plot.plot_cox_conditional.omics_name) != '':
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132 #set $name = str($plot.plot_cox_conditional.omics_name.replace(" ", "_"))
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133 --omics_train input/train/${name}.csv
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134 --omics_test input/test/${name}.csv
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135 #else
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136 --omics_train input/train/main.csv
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137 --omics_test input/test/main.csv
0
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138 #end if
3
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139 --surv_time_var $surv_time_var
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140 --surv_event_var $surv_event_var
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141 #if str($plot.plot_cox_conditional.clinical_variables) != '':
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142 --clinical_variables $str($plot.plot_cox_conditional.clinical_variables)
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143 #end if
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144 --top_features $plot.plot_cox_conditional.top_features
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145 --event_value $plot.plot_cox_conditional.event_value
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146 #if str($plot.plot_cox_conditional.crossval_conditional.crossval) == 'yes':
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147 --crossval
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148 #end if
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149 #if str($plot.plot_cox_conditional.crossval_conditional.crossval) == 'yes':
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150 --n_splits $plot.plot_cox_conditional.crossval_conditional.n_splits
0
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151 #end if
3
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152 --random_state 42
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153 --output_dir plots
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154 --format $plot.plot_cox_conditional.format
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155 --dpi $plot.plot_cox_conditional.dpi
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156 #end if
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157 #end if
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158 #if str($plot.plot_scatter_conditional.plot_scatter) == 'yes':
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159 && python $__tool_directory__/flexynesis_plot.py
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160 --plot_type scatter
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161 --labels output/job.predicted_labels.csv
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162 #if str($surv_event_var) != '':
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163 --target_value $target_variables,$surv_event_var
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164 #else
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165 --target_value $target_variables
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166 #end if
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167 --output_dir plots
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168 --format $plot.plot_scatter_conditional.format
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169 --dpi $plot.plot_scatter_conditional.dpi
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170 #end if
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171 #if str($plot.plot_concordance_conditional.plot_concordance) == 'yes':
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172 && python $__tool_directory__/flexynesis_plot.py
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173 --plot_type concordance_heatmap
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174 --labels output/job.predicted_labels.csv
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175 #if str($surv_event_var) != '':
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176 --target_value $target_variables,$surv_event_var
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177 #else
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178 --target_value $target_variables
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179 #end if
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180 --output_dir plots
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181 --format $plot.plot_concordance_conditional.format
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182 --dpi $plot.plot_concordance_conditional.dpi
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183 #end if
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184 #if str($plot.plot_pr_curves_conditional.plot_pr_curves) == 'yes':
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185 && python $__tool_directory__/flexynesis_plot.py
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186 --plot_type pr_curve
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187 --labels output/job.predicted_labels.csv
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188 #if str($surv_event_var) != '':
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189 --target_value $target_variables,$surv_event_var
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190 #else
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191 --target_value $target_variables
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192 #end if
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193 --output_dir plots
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194 --format $plot.plot_pr_curves_conditional.format
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195 --dpi $plot.plot_pr_curves_conditional.dpi
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196 #end if
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197 #if str($plot.plot_roc_curves_conditional.plot_roc_curves) == 'yes':
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198 && python $__tool_directory__/flexynesis_plot.py
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199 --plot_type roc_curve
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200 --labels output/job.predicted_labels.csv
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201 #if str($surv_event_var) != '':
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202 --target_value $target_variables,$surv_event_var
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203 #else
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204 --target_value $target_variables
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205 #end if
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206 --output_dir plots
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207 --format $plot.plot_roc_curves_conditional.format
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208 --dpi $plot.plot_roc_curves_conditional.dpi
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209 #end if
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210 #if str($plot.plot_boxplot_conditional.plot_boxplot) == 'yes':
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211 && python $__tool_directory__/flexynesis_plot.py
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212 --plot_type box_plot
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213 --labels output/job.predicted_labels.csv
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214 #if str($surv_event_var) != '':
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215 --target_value $target_variables,$surv_event_var
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216 #else
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217 --target_value $target_variables
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218 #end if
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219 --output_dir plots
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220 --format $plot.plot_boxplot_conditional.format
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221 --dpi $plot.plot_boxplot_conditional.dpi
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222 #end if
0
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223 ]]></command>
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224 <inputs>
3
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225 <expand macro="commercial_use_param"/>
0
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226 <conditional name="training_type">
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227 <param name="model" type="select" label="Type of Analysis" >
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228 <option value="s_train">Supervised training</option>
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229 <option value="us_train">Unsupervised Training</option>
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230 <option value="cm_train">Cross-modality Training</option>
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231 </param>
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232 <when value="s_train">
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233 <expand macro="main_inputs"/>
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234 <repeat name="omics" min="0" title="Multiple omics layers?">
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235 <expand macro="extra_inputs"/>
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236 </repeat>
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237 <conditional name="model_class" label="Model class">
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238 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
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239 <option value="DirectPred">DirectPred</option>
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240 <option value="GNN">GNN</option>
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241 <option value="MultiTripletNetwork">MultiTripletNetwork</option>
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242 <option value="RandomForest">RandomForest</option>
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243 <option value="SVM">SVM</option>
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244 <option value="RandomSurvivalForest">RandomSurvivalForest</option>
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245 <option value="XGBoost">XGBoost</option>
0
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246 </param>
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247 <when value="DirectPred"/>
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248 <when value="GNN">
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249 <param argument="--gnn_conv_type" type="select" label="Which graph convolution type to use.">
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250 <option value="GC">GC</option>
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251 <option value="GCN">GCN</option>
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252 <option value="SAGE">SAGE</option>
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253 </param>
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254 <param argument="--string_organism" type="select" label="STRING DB organism">
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255 <option value="9606">Homo sapiens</option>
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256 <option value="10090">Mus musculus</option>
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257 <option value="10116">Rattus norvegicus</option>
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258 <option value="9544">Macaca mulatta</option>
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259 </param>
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260 <param argument="--string_node_name" type="select" label="String node name" >
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261 <option value="gene_name">Gene name</option>
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262 <option value="gene_id">Gene id</option>
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263 </param>
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264 </when>
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265 <when value="MultiTripletNetwork"/>
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266 <when value="RandomForest"/>
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267 <when value="SVM"/>
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268 <when value="RandomSurvivalForest"/>
1
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269 <when value="XGBoost"/>
0
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270 </conditional>
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271 <param argument="--target_variables" type="text" label="Target variables" help="Which variables in 'clin.csv' to use for predictions, comma-separated if multiple.">
3
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272 <expand macro="sanitizer_printable"/>
0
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273 </param>
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274 <param argument="--surv_event_var" type="text" label="Survival event" help="Which column in 'clin.csv' to use as event/status indicator for survival modeling.">
3
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275 <expand macro="sanitizer_printable"/>
0
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276 </param>
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277 <param argument="--surv_time_var" type="text" label="Survival time" help="Which column in 'clin.csv' to use as time/duration indicator for survival modeling.">
3
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278 <expand macro="sanitizer_printable"/>
0
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279 </param>
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280 <expand macro="advanced"/>
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281 </when>
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282 <when value="us_train">
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283 <expand macro="main_inputs"/>
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284 <repeat name="omics" min="0" title="Multiple omics layers?">
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285 <expand macro="extra_inputs"/>
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286 </repeat>
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287 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
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288 <option value="supervised_vae">supervised_vae</option>
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289 </param>
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290 <expand macro="advanced"/>
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291 </when>
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292 <when value="cm_train">
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293 <expand macro="main_inputs"/>
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294 <param name="layer_main" type="select" label="Use this omics data as input or output layer?">
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295 <option value="input">Input</option>
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296 <option value="output">output</option>
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297 </param>
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298 <repeat name="omics" min="0" title="Multiple omics layers?">
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299 <expand macro="extra_inputs"/>
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300 <param name="layer" type="select" label="Use this omics data as input or output layer?">
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301 <option value="input">Input</option>
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302 <option value="output">output</option>
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303 </param>
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304 </repeat>
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305 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
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306 <option value="CrossModalPred">CrossModalPred</option>
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307 </param>
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308 <expand macro="advanced"/>
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309 </when>
0
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310 </conditional>
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311 <section name="plot" title="Visualization">
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312 <conditional name="plot_embeddings_conditional">
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313 <param name="plot_embeddings" type="select" label="Generate embeddings plot?" help="Generate PCA or UMAP plot of the test dataset">
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314 <option value="yes">Yes</option>
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315 <option value="no" selected="true">No</option>
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316 </param>
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317 <when value="no">
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318 </when>
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319 <when value="yes">
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320 <param name="method" type="select" label="Transformation method">
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321 <option value="pca" selected="true">PCA</option>
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322 <option value="umap">UMAP</option>
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323 </param>
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324 <expand macro="plots_common_param"/>
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325 </when>
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326 </conditional>
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327 <conditional name="plot_km_conditional">
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328 <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">
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329 <option value="yes">Yes</option>
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330 <option value="no" selected="true">No</option>
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331 </param>
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332 <when value="no">
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333 </when>
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334 <when value="yes">
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335 <param name="event_value" type="text" label="Event value" optional="false" help="The value in the event column that indicates an event (e.g. death) has occurred.">
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336 <expand macro="sanitizer_printable"/>
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337 </param>
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338 <expand macro="plots_common_param"/>
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339 </when>
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340 </conditional>
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341 <conditional name="plot_cox_conditional">
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342 <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.">
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343 <option value="yes">Yes</option>
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344 <option value="no" selected="true">No</option>
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345 </param>
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346 <when value="no">
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347 </when>
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348 <when value="yes">
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349 <param name="omics_name" type="text" label="Omics layer to use for cox input" optional="false" help="If not specified, the first omics layer will be used.">
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350 <expand macro="sanitizer_printable"/>
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351 </param>
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352 <param name="clinical_variables" type="text" label="Clinical covariates" optional="true" help="Comma-separated list of clinical covariates to include in the Cox model (e.g SEX, AGE, ...).">
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353 <expand macro="sanitizer_printable"/>
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354 </param>
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355 <param argument="--top_features" type="integer" min="1" value="20" label="Number of top important features to include in Cox model"/>
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356 <param name="event_value" type="text" label="Event value" optional="false" help="The value in the event column that indicates an event (e.g. death) has occurred.">
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357 <expand macro="sanitizer_printable"/>
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358 </param>
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359 <conditional name="crossval_conditional">
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360 <param name="crossval" type="select" label="Performs K-fold cross-validation?">
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361 <option value="yes">Yes</option>
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362 <option value="no" selected="true">No</option>
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363 </param>
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parents: 1
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364 <when value="yes">
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365 <param name="n_splits" type="integer" min="2" value="5" label="Number of folds for cross-validation"/>
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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366 </when>
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parents: 1
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367 <when value="no"/>
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368 </conditional>
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parents: 1
diff changeset
369 <expand macro="plots_common_param"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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370 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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371 </conditional>
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372 <conditional name="plot_scatter_conditional">
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373 <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.">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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374 <option value="yes">Yes</option>
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375 <option value="no" selected="true">No</option>
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376 </param>
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377 <when value="no">
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378 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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379 <when value="yes">
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380 <expand macro="plots_common_param"/>
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381 </when>
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382 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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383 <conditional name="plot_concordance_conditional">
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384 <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.">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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385 <option value="yes">Yes</option>
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386 <option value="no" selected="true">No</option>
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387 </param>
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388 <when value="no">
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389 </when>
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parents: 1
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390 <when value="yes">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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391 <expand macro="plots_common_param"/>
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392 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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393 </conditional>
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394 <conditional name="plot_pr_curves_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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395 <param name="plot_pr_curves" type="select" label="Generate precision-recall curves plot?" help="Generates precision-recall curves for all available targets.">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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396 <option value="yes">Yes</option>
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397 <option value="no" selected="true">No</option>
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398 </param>
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diff changeset
399 <when value="no">
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400 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
401 <when value="yes">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
402 <expand macro="plots_common_param"/>
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parents: 1
diff changeset
403 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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404 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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405 <conditional name="plot_roc_curves_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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406 <param name="plot_roc_curves" type="select" label="Generate ROC curves plot?" help="Generates ROC curves for all available targets.">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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407 <option value="yes">Yes</option>
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408 <option value="no" selected="true">No</option>
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409 </param>
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410 <when value="no">
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411 </when>
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412 <when value="yes">
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413 <expand macro="plots_common_param"/>
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414 </when>
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415 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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416 <conditional name="plot_boxplot_conditional">
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417 <param name="plot_boxplot" type="select" label="Generate boxplot?" help="Generates a boxplot for all available targets.">
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418 <option value="yes">Yes</option>
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419 <option value="no" selected="true">No</option>
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420 </param>
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421 <when value="no">
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422 </when>
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423 <when value="yes">
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424 <expand macro="plots_common_param"/>
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425 </when>
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426 </conditional>
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427 </section>
0
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428 </inputs>
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429 <outputs>
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430 <collection name="results" type="list" label="${tool.name} on ${on_string}: results">
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431 <discover_datasets pattern="(?P&lt;name&gt;.+)\.csv$" format="csv" directory="output"/>
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432 </collection>
3
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433 <collection name="plots" type="list" label="${tool.name} on ${on_string}: embeddings plots">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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434 <discover_datasets pattern="__name_and_ext__" directory="plots"/>
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435 <filter>plot['plot_embeddings_conditional']['plot_embeddings'] == 'yes' or plot['plot_km_conditional']['plot_km'] == 'yes' or plot['plot_cox_conditional']['plot_cox'] == 'yes' or plot['plot_scatter_conditional']['plot_scatter'] == 'yes' or plot['plot_concordance_conditional']['plot_concordance'] == 'yes' or plot['plot_pr_curves_conditional']['plot_pr_curves'] == 'yes' or plot['plot_roc_curves_conditional']['plot_roc_curves'] == 'yes' or plot['plot_boxplot_conditional']['plot_boxplot'] == 'yes'</filter>
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436 </collection>
0
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437 </outputs>
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438 <tests>
3
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439 <!-- test 1: Supervised training with GEX and CNV data, DirectPred model, Erlotinib target -->
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440 <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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441 <param name="non_commercial_use" value="True"/>
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442 <conditional name="training_type">
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443 <param name="model" value="s_train"/>
1
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444 <param name="train_clin" value="train/clin" ftype="csv"/>
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445 <param name="test_clin" value="test/clin" ftype="csv"/>
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446 <param name="train_omics_main" value="train/gex" ftype="csv"/>
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447 <param name="test_omics_main" value="test/gex" ftype="csv"/>
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448 <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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449 <repeat name="omics">
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parents: 0
diff changeset
450 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
451 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
452 <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
453 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
454 <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
455 <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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parents: 0
diff changeset
456 </conditional>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
457 <param name="target_variables" value="Erlotinib"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
458 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
459 <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
460 </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
461 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
462 <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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parents:
diff changeset
463 <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
464 <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
465 <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
466 </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
467 </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
468 <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
469 <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
470 <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
471 </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
472 </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
473 <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
474 <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
475 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
476 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
477 <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
478 </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
479 </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
480 <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
481 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
482 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
483 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
484 <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
485 </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
486 </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
487 <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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diff changeset
488 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
489 <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
490 </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
491 </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
492 <element name="job.feature_logs.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
493 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
494 <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
495 </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
496 </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
497 <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
498 <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
499 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
500 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
501 </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
502 </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
503 <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
504 <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
505 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
506 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
507 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
508 </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
509 </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
510 </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
511 </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
512 <!-- 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
bgruening
parents: 1
diff changeset
513 <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
514 <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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parents:
diff changeset
515 <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
516 <param name="model" value="s_train"/>
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
517 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
518 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
519 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
520 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
521 <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
522 <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
523 <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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parents: 0
diff changeset
524 </conditional>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
525 <param name="target_variables" value="Erlotinib"/>
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
526 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
527 <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
528 </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
529 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
530 <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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parents:
diff changeset
531 <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
532 <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
533 <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
534 </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
535 </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
536 <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
537 <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
538 <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
539 </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
540 </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
541 <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
542 <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
543 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
544 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
545 <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
546 </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
547 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
548 <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
549 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
550 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
551 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
552 <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
553 </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
554 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
555 <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
556 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
557 <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
558 </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
559 </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
560 <element name="job.predicted_labels">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
561 <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
562 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
563 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
564 </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
565 </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
566 <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
567 <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
568 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
569 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
570 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
571 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
572 </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
573 </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
574 </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
575 <!-- 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
bgruening
parents: 1
diff changeset
576 <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
577 <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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parents:
diff changeset
578 <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
579 <param name="model" value="s_train"/>
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
580 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
581 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
582 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
583 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
584 <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
585 <repeat name="omics">
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 <param name="train_omics" value="train/cnv" ftype="csv"/>
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="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
588 <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
589 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
590 <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
591 <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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parents: 0
diff changeset
592 </conditional>
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 <param name="target_variables" value="Irinotecan"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
594 <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
595 <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
596 </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
597 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
598 <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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parents:
diff changeset
599 <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
600 <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
601 <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
602 </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
603 </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
604 <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
605 <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
606 <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
607 </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
608 </element>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
609 <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
610 <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
611 <has_text_matching expression="Irinotecan,0,,bar,A2M,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
612 <has_text_matching expression="Irinotecan,0,,bar,ABCC4,"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
613 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
614 </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
615 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
616 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
617 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
618 <has_text_matching expression="Irinotecan,0,,bar,A2M,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
619 <has_text_matching expression="Irinotecan,0,,bar,ABCC4,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
620 <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
621 </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
622 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
623 <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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diff changeset
624 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
625 <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
626 </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
627 </element>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
628 <element name="job.feature_logs.omics_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
629 <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
630 <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
631 </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
632 </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
633 <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
634 <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
635 <has_text_matching expression="source_dataset:A-704,Irinotecan,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
636 <has_text_matching expression="target_dataset:KMRC-20,Irinotecan,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
637 </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
638 </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
639 <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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diff changeset
640 <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
641 <has_text_matching expression="DirectPred,Irinotecan,numerical,mse,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
642 <has_text_matching expression="DirectPred,Irinotecan,numerical,r2,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
643 <has_text_matching expression="DirectPred,Irinotecan,numerical,pearson_corr,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
644 </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
645 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
646 </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
647 </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
648 <!-- 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
649 <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
650 <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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parents:
diff changeset
651 <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
652 <param name="model" value="us_train"/>
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
653 <param name="train_clin" value="train/clin" ftype="csv"/>
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 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
655 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
656 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
657 <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
658 <repeat name="omics">
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="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
660 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
661 <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
662 </repeat>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
663 <param name="model_class" value="supervised_vae"/>
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
664 <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
665 <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
666 </section>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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667 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
668 <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
669 <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
670 <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
671 <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
672 </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
673 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
674 <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
675 <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
676 <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
677 </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
678 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
679 <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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diff changeset
680 <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
681 <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
682 </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
683 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
684 <element name="job.feature_logs.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
685 <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
686 <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
687 </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
688 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
689 </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
690 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
691 <!-- 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
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parents: 1
diff changeset
692 <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
693 <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
694 <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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695 <param name="model" value="cm_train"/>
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
696 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
697 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
698 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
699 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
700 <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
701 <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
702 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
703 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
704 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
705 <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
706 <param name="layer" value="output"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
707 </repeat>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
708 <param name="model_class" value="CrossModalPred"/>
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
709 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
710 <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
711 </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
712 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
713 <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
714 <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
715 <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
716 <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
717 </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
718 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
719 <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
720 <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
721 <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
722 </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
723 </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
724 <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
725 <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
726 <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
727 </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
728 </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
729 <element name="job.feature_logs.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
730 <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
731 <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
732 </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
733 </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
734 <element name="job.test_decoded.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
735 <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
736 <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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parents:
diff changeset
737 </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
738 </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
739 <element name="job.train_decoded.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
740 <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
741 <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
742 </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
743 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
744 </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
745 </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
746 <!-- 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
747 <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
748 <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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parents:
diff changeset
749 <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
750 <param name="model" value="s_train"/>
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
751 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
752 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
753 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
754 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
755 <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
756 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
757 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
758 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
759 <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
760 </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
761 <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
762 <param name="model_class" value="GNN"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
763 <param name="gnn_conv_type" value="GC"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
764 <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
765 <param name="string_node_name" value="gene_name"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
766 </conditional>
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
767 <param name="target_variables" value="Erlotinib"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
768 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
769 <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
770 </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
771 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
772 <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
773 <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
774 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
775 <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
776 </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
777 </element>
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_train">
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>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
783 <element name="job.feature_importance.GradientShap">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
784 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
785 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
786 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
787 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
788 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
789 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
790 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
791 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
792 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
793 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
794 <has_text_matching expression="IntegratedGradients"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
795 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
796 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
797 <element name="job.feature_logs.bar">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
798 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
799 <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
800 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
801 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
802 <element name="job.feature_logs.omics_foo">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
803 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
804 <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
805 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
806 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
807 <element name="job.predicted_labels">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
808 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
809 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
810 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
811 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
812 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
813 <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
814 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
815 <has_text_matching expression="GNN,Erlotinib,numerical,mse,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
816 <has_text_matching expression="GNN,Erlotinib,numerical,r2,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
817 <has_text_matching expression="GNN,Erlotinib,numerical,pearson_corr,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
818 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
819 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
820 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
821 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
822 <!-- 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
bgruening
parents: 1
diff changeset
823 <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
824 <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
825 <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
826 <param name="model" value="us_train"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
827 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
828 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
829 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
830 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
831 <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
832 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
833 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
834 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
835 <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
836 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
837 <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
838 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
839 <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
840 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
841 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
842 <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
843 <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
844 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
845 <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
846 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
847 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
848 <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
849 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
850 <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
851 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
852 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
853 <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
854 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
855 <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
856 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
857 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
858 <element name="job.feature_logs.omics_f_oo">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
859 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
860 <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
861 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
862 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
863 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
864 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
865 <!-- 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
866 <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
867 <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
868 <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
869 <param name="model" value="s_train"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
870 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
871 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
872 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
873 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
874 <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
875 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
876 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
877 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
878 <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
879 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
880 <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
881 <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
882 </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
883 <param name="target_variables" value="Erlotinib"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
884 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
885 <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
886 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
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diff changeset
887 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
888 <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
889 <element name="job.stats">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
890 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
891 <has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,mse,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
892 <has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,r2,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
893 <has_text_matching expression="XGBoostRegressor,Erlotinib,numerical,pearson_corr,"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
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diff changeset
894 </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
895 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
896 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
897 </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
898 <!-- 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
899 <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
900 <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
901 <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
902 <param name="model" value="s_train"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
903 <param name="train_clin" value="train/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
904 <param name="test_clin" value="test/clin" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
905 <param name="train_omics_main" value="train/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
906 <param name="test_omics_main" value="test/gex" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
907 <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
908 <repeat name="omics">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
909 <param name="train_omics" value="train/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
910 <param name="test_omics" value="test/cnv" ftype="csv"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
911 <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
912 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
913 <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
914 <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
915 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
916 <param name="target_variables" value="Erlotinib"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
917 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
918 <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
919 <param name="feature_importance_method" value="IntegratedGradients"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
920 <param name="val_size" value="0.2"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
921 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
922 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
923 <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
924 <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
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 <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
927 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
928 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
929 <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
930 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
931 <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
932 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
933 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
934 <element name="job.feature_importance.IntegratedGradients">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
935 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
936 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
937 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
938 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
939 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
940 <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
941 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
942 <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
943 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
944 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
945 <element name="job.feature_logs.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
946 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
947 <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
948 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
949 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
950 <element name="job.predicted_labels">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
951 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
952 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
953 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
954 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
955 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
956 <element name="job.stats">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
957 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
958 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
959 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
960 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
961 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
962 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
963 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
964 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
965 <!-- 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
966 <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
967 <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
968 <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
969 <param name="model" value="s_train"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
970 <param name="train_clin" value="train/clin" ftype="csv"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
971 <param name="test_clin" value="test/clin" ftype="csv"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
972 <param name="train_omics_main" value="train/gex" ftype="csv"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
973 <param name="test_omics_main" value="test/gex" ftype="csv"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
974 <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
975 <repeat name="omics">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
976 <param name="train_omics" value="train/cnv" ftype="csv"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
977 <param name="test_omics" value="test/cnv" ftype="csv"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
978 <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
979 </repeat>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
980 <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
981 <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
982 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
983 <param name="target_variables" value="Erlotinib"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
984 <section name="advanced">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
985 <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
986 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
987 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
988 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
989 <conditional name="plot_embeddings_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
990 <param name="plot_embeddings" value="yes"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
991 <param name="method" value="pca"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
992 <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
993 <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
994 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
995 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
996 <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
997 <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
998 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
999 <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
1000 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1001 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1002 <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
1003 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1004 <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
1005 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1006 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1007 <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
1008 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1009 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1010 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1011 <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
1012 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1013 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1014 <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
1015 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1016 <has_text_matching expression="Erlotinib,0,,bar,A2M,"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1017 <has_text_matching expression="Erlotinib,0,,bar,ABCC4,"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1018 <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
1019 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1020 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1021 <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
1022 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1023 <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
1024 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1025 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1026 <element name="job.feature_logs.omics_foo">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1027 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1028 <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
1029 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1030 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1031 <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
1032 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1033 <has_text_matching expression="source_dataset:A-704,Erlotinib,"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1034 <has_text_matching expression="target_dataset:KMRC-20,Erlotinib,"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1035 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1036 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1037 <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
1038 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1039 <has_text_matching expression="DirectPred,Erlotinib,numerical,mse,"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1040 <has_text_matching expression="DirectPred,Erlotinib,numerical,r2,"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1041 <has_text_matching expression="DirectPred,Erlotinib,numerical,pearson_corr,"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1042 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1043 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1044 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1045 <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
1046 <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
1047 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1048 <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
1049 <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
1050 <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
1051 <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
1052 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1053 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1054 <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
1055 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1056 <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
1057 <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
1058 <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
1059 <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
1060 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1061 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1062 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1063 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1064 <!-- 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
1065 <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
1066 <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
1067 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1068 <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
1069 <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
1070 <param name="event_value" value="1:DECEASED"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1071 <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
1072 <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
1073 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1074 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1075 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1076 <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
1077 <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
1078 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1079 <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
1080 <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
1081 <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
1082 <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
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 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1086 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1087 <!-- 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
1088 <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
1089 <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
1090 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1091 <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
1092 <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
1093 <param name="omics_name" value="bar"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1094 <param name="clinical_variables" value="Crizotinib, Erlotinib"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1095 <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
1096 <param name="event_value" value="1:DECEASED"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1097 <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
1098 <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
1099 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1100 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1101 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1102 <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
1103 <element name="job.final_model_cox_hazard_ratios">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1104 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1105 <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
1106 <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
1107 <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
1108 <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
1109 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1110 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1111 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1112 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1113 <!-- 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
1114 <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
1115 <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
1116 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1117 <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
1118 <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
1119 <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
1120 <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
1121 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1122 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1123 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1124 <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
1125 <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
1126 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1127 <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
1128 <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
1129 <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
1130 <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
1131 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1132 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1133 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1134 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1135 <!-- 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
1136 <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
1137 <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
1138 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1139 <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
1140 <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
1141 <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
1142 <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
1143 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1144 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1145 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1146 <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
1147 <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
1148 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1149 <has_image_center_of_mass center_of_mass="1547,1620" eps="30"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1150 <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
1151 <has_image_height height="3060" delta="50"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1152 <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
1153 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1154 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1155 <element name="job.predicted_labels_concordance_OS_STATUS">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1156 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1157 <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
1158 <has_image_height height="2558" delta="50"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1159 <has_image_width width="2794" delta="50"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1160 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1161 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1162 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1163 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1164 <!-- 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
1165 <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
1166 <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
1167 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1168 <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
1169 <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
1170 <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
1171 <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
1172 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1173 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1174 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1175 <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
1176 <element name="job.predicted_labels_pr_curves_OS_STATUS">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1177 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1178 <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
1179 <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
1180 <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
1181 <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
1182 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1183 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1184 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1185 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1186 <!-- 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
1187 <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
1188 <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
1189 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1190 <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
1191 <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
1192 <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
1193 <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
1194 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1195 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1196 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1197 <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
1198 <element name="job.predicted_labels_roc_curves_OS_STATUS">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1199 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1200 <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
1201 <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
1202 <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
1203 <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
1204 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1205 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1206 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1207 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1208 <!-- 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
1209 <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
1210 <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
1211 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1212 <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
1213 <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
1214 <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
1215 <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
1216 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1217 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1218 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1219 <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
1220 <element name="job.predicted_labels_box_plot_OS_STATUS_0_LIVING">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1221 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1222 <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
1223 <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
1224 <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
1225 <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
1226 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1227 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1228 <element name="job.predicted_labels_box_plot_OS_STATUS_1_DECEASED">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1229 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1230 <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
1231 <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
1232 <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
1233 <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
1234 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1235 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1236 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1237 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1238 <!-- 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
1239 <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
1240 <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
1241 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1242 <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
1243 <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
1244 <param name="omics_name" value="bar"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1245 <param name="clinical_variables" value="Crizotinib, Erlotinib"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1246 <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
1247 <param name="event_value" value="1:DECEASED"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1248 <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
1249 <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
1250 <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
1251 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1252 <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
1253 <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
1254 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1255 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1256 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1257 <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
1258 <element name="job.final_model_cox_hazard_ratios">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1259 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1260 <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
1261 <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
1262 <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
1263 <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
1264 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1265 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1266 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1267 </test>
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
1268 </tests>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1269 <help><![CDATA[
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
1270 @COMMON_HELP@
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
1271
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1272 .. 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
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parents:
diff changeset
1273 :width: 600
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1274
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1275 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1276
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1277 **Input Files**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1278
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1279 **clin.csv**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1280
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
1281 clin.csv 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
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diff changeset
1282
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1283 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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diff changeset
1284
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1285 ======== === === ===
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1286 , v1 v2 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1287 -------- --- --- ---
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1288 sample1 a b ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1289 -------- --- --- ---
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1290 sample2 c d ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1291 -------- --- --- ---
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1292 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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diff changeset
1293 -------- --- --- ---
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1294 ... ... ... ...
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1295 ======== === === ===
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1296
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1297 .
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1298
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1299 **omics.csv**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1300
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
1301 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.csv. They don't have to be completely identical or in the same order. Samples from the clin.csv 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
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diff changeset
1302
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1303 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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diff changeset
1304
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1305 ===== ======= ======= ======= =======
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1306 , sample1 sample2 sample3 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1307 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1308 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
1309 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1310 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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diff changeset
1311 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1312 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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diff changeset
1313 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1314 ... ... ... ... ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1315 ===== ======= ======= ======= =======
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1316
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1317 .
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1318
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
1319 .. 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
1320
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1321 **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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diff changeset
1322
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
1323 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.csv 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
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diff changeset
1324
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1325 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1326
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1327 **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
1328
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1329 **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
1330
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1331 * clin.csv and omics.csv 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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diff changeset
1332 * 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
1333 * 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
1334
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
1335 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
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diff changeset
1336
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1337 **Regression:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1338
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1339
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1340 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
1341
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1342 **Classification:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1343
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1344
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1345 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
1346
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1347 **Survival Analysis:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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1348
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1349
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1350 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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diff changeset
1351 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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1352
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1353 .. class:: infomark
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1354
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1355 **Note:** Flexynesis can be trained with multiple target variables, which can be a mixture of regression/classification/survival tasks.
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1356
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1357 .. class:: infomark
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1358
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1359 **Note:** For the supervised tasks, the user can easily switch between different model architectures.
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1360
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1361 .. class:: infomark
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1362
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1363 **Note:** If you choose **MultiTripletNetwork** model, the first target variable should be a categorical variable.
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1364
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1365 .. class:: infomark
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1366
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1367 **Note:** If you choose **GNN** model, the features should have the same naming convention between different omics modalities.
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1368
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1369 .. class:: infomark
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1370
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1371 **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.
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1372
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1373 -----
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1374
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1375 **Unsupervised Training**
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1376
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1377 In the absence of any target variables or survival variables, you can use a VAE architecture to carry out unsupervised training.
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1378
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1379 -----
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1380
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1381 **Cross-modality Training**
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1382
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1383 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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1384
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1385 .. class:: infomark
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1386
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1387 **Note:** if you use same input and output layers, it will be the same as unsupervised training.
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1389 -----
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1391 .. class:: infomark
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1392
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1393 **Modality fusion:**
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1394
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1395 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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1396
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1397 .. _Documentation: https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/site/
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1398 .. _copyright holders: https://github.com/BIMSBbioinfo/flexynesis
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1399 ]]></help>
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1400 <expand macro="creator"/>
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1401 <expand macro="citations"/>
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1402 </tool>