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annotate flexynesis.xml @ 5:466b593fd87e draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
author bgruening
date Fri, 04 Jul 2025 14:57:40 +0000
parents 1a5f8cedda43
children 33816f44fc7d
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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>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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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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466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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14 ln -s '$train_clin' input/train/clin.tabular &&
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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15 python $__tool_directory__/convert.py input/train/clin.tabular input/train/clin.csv &&
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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17 ln -s '$test_clin' input/test/clin.tabular &&
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18 python $__tool_directory__/convert.py input/test/clin.tabular input/test/clin.csv &&
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20 #if str($assay_main) != '':
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21 #set $name = str($assay_main.replace(" ", "_"))
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466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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22 ln -s '$train_omics_main' input/train/${name}.tabular &&
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23 python '$__tool_directory__/convert.py' input/train/${name}.tabular input/train/${name}.csv &&
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25 ln -s '$test_omics_main' input/test/${name}.tabular &&
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26 python '$__tool_directory__/convert.py' input/test/${name}.tabular input/test/${name}.csv &&
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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27
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28 #set $data_names = [$name]
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29 #else
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30 ln -s '$train_omics_main' input/train/main.tabular &&
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31 python '$__tool_directory__/convert.py' input/train/main.tabular input/train/main.csv &&
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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32 ln -s '$test_omics_main' input/test/main.tabular &&
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33 python '$__tool_directory__/convert.py' input/test/main.tabular input/test/main.csv &&
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34 #set $data_names = ['main']
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35 #end if
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36 #if str($training_type.model) == 'cm_train':
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37 #if str($layer_main) == 'input':
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38 #set $input_layers = $data_names
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39 #set $output_layers = []
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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40 #else
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41 #set $input_layers = []
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42 #set $output_layers = $data_names
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43 #end if
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44 #end if
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45 #for $i, $element in enumerate($omics)
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46 #if str($element.train_omics) != 'None' and str($element.test_omics) != 'None':
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47 #if str($element.assay) != '':
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48 #set $i = str($element.assay.replace(" ", "_"))
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49 #end if
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50 ln -s '${element.train_omics}' input/train/omics_${i}.tabular &&
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51 python '$__tool_directory__/convert.py' input/train/omics_${i}.tabular input/train/omics_${i}.csv &&
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53 ln -s '${element.test_omics}' input/test/omics_${i}.tabular &&
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54 python '$__tool_directory__/convert.py' input/test/omics_${i}.tabular input/test/omics_${i}.csv &&
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55
0
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56 $data_names.append("omics_" + str($i))
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57 #if str($training_type.model) == 'cm_train':
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58 #if str($element.layer) == 'input':
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59 $input_layers.append("omics_" + str($i))
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60 #else
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61 $output_layers.append("omics_" + str($i))
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62 #end if
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63 #end if
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64 #end if
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65 #end for
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66 ## set target variables
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67 #if str($training_type.model) == 's_train':
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68 #if len($targets) > 0:
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69 target_variables="" &&
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70 #for $i, $element in enumerate($targets)
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71 target_name=`$__tool_directory__/index_to_name.py input/train/clin.csv $element.target_variables` &&
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72 #if $i == 0:
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73 target_variables="\$target_name" &&
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74 #else:
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75 target_variables="\$target_variables,\$target_name" &&
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76 #end if
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77 #end for
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78 echo "Target variables: \$target_variables" &&
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79 #end if
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80 ## set survival variables
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81 #if str($surv_event_var) != 'None' and str($surv_time_var) != 'None':
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82 surv_event_var=`$__tool_directory__/index_to_name.py input/train/clin.csv $surv_event_var` &&
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83 echo "Survival event variable: \$surv_event_var" &&
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84 surv_time_var=`$__tool_directory__/index_to_name.py input/train/clin.csv $surv_time_var` &&
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85 echo "Survival time variable: \$surv_time_var" &&
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86 #end if
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87 ## set target value for plots
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88 #if str($surv_event_var) != 'None' and str($surv_time_var) != 'None' and len($targets) > 0:
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89 target_value="\$target_variables,\$surv_event_var" &&
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90 echo "Target value for plots: \$target_value" &&
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91 #else if str($surv_event_var) == 'None' and str($surv_time_var) == 'None' and len($targets) > 0:
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92 target_value="\$target_variables" &&
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93 echo "Target value for plots: \$target_value" &&
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94 #else if str($surv_event_var) != 'None' and str($surv_time_var) != 'None' and len($targets) == 0:
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95 target_value="\$surv_event_var" &&
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96 echo "Target value for plots: \$target_value" &&
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97 #end if
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98 #end if
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99
3
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100 flexynesis
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101 --data_path input
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102 --outdir output
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103 --model_class $model_class
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104 #if str($model_class) == 'GNN':
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105 --gnn_conv_type $gnn_conv_type
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106 --string_organism $string_organism
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107 --string_node_name $string_node_name
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108 #end if
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109 #if str($training_type.model) == 's_train':
5
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110 #if len($targets) > 0:
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111 --target_variables \$target_variables
3
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112 #end if
5
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113 #if str($surv_event_var) != 'None' and str($surv_time_var) != 'None':
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114 --surv_event_var \$surv_event_var
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115 --surv_time_var \$surv_time_var
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116 #end if
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117 #end if
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118 #if str($training_type.model) == 'cm_train':
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119 --input_layers $str(",".join($input_layers))
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120 --output_layers $str(",".join($output_layers))
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121 #end if
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122 --fusion_type $fusion_type
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123 --hpo_iter $hpo_iter
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124 --val_size $val_size
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125 --finetuning_samples $finetuning_samples
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126 --variance_threshold $variance_threshold
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127 --correlation_threshold $correlation_threshold
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128 --subsample $subsample
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129 --features_min $features_min
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130 --features_top_percentile $features_top_percentile
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131 --data_types $str(",".join($data_names))
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132 --early_stop_patience $early_stop_patience
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133 --hpo_patience $hpo_patience
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134 $log_transform
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135 $use_loss_weighting
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136 $use_cv
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137 $evaluate_baseline_performance
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138 --feature_importance_method $feature_importance_method
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139 \${GALAXY_FLEXYNESIS_EXTRA_ARGUMENTS}
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140
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141 ## convert flexynesis output files to tabular format
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142 && for file in output/*.csv; do
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143 if [ -f "\$file" ]; then
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144 basename="\${file%.csv}";
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145 python $__tool_directory__/convert.py "\$file" "\${basename}.tabular";
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146 echo "Converted \$file to \${basename}.tabular";
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147 fi
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148 done
3
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149 #if str($plot.plot_embeddings_conditional.plot_embeddings) == 'yes':
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150 && python $__tool_directory__/flexynesis_plot.py
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151 --plot_type dimred
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152 --embeddings output/job.embeddings_test.tabular
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153 --labels output/job.predicted_labels.tabular
3
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154 --method $plot.plot_embeddings_conditional.method
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155 #if str($training_type.model) == 's_train':
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156 #if len($targets) > 0 or (str($surv_event_var) != 'None' and str($surv_time_var) != 'None'):
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157 --target_value \$target_value
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158 #end if
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159 #end if
3
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160 --output_dir plots
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161 --format $plot.plot_embeddings_conditional.format
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162 --dpi $plot.plot_embeddings_conditional.dpi
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163 #end if
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164 #if str($plot.plot_km_conditional.plot_km) == 'yes':
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165 #if str($surv_event_var) == '' or str($surv_time_var) == '':
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166 && echo "Survival event and time variables must be specified for Kaplan-Meier plots."
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167 && exit 1
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168 #else
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169 && python $__tool_directory__/flexynesis_plot.py
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170 --plot_type kaplan_meier
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171 --labels output/job.predicted_labels.tabular
3
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172 --survival_data input/test/clin.csv
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173 --surv_event_var \$surv_event_var
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174 --surv_time_var \$surv_time_var
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175 --event_value $plot.plot_km_conditional.event_value
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176 --output_dir plots
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177 --format $plot.plot_km_conditional.format
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178 --dpi $plot.plot_km_conditional.dpi
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179 #end if
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180 #end if
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181 #if str($plot.plot_cox_conditional.plot_cox) == 'yes':
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182 #if str($surv_event_var) == '' or str($surv_time_var) == '':
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183 && echo "Survival event and time variables must be specified for cox plots."
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184 && exit 1
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185 #else
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186 && python $__tool_directory__/flexynesis_plot.py
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187 --plot_type cox
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188 --model output/job.final_model.pth
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189 --clinical_train input/train/clin.csv
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190 --clinical_test input/test/clin.csv
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191 #if str($plot.plot_cox_conditional.omics_name) != '':
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192 #set $name = str($plot.plot_cox_conditional.omics_name.replace(" ", "_"))
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193 --omics_train input/train/${name}.csv
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194 --omics_test input/test/${name}.csv
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195 #else
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196 --omics_train input/train/main.csv
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197 --omics_test input/test/main.csv
0
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198 #end if
5
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199 --surv_time_var \$surv_time_var
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200 --surv_event_var \$surv_event_var
3
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201 #if str($plot.plot_cox_conditional.clinical_variables) != '':
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202 --clinical_variables $str($plot.plot_cox_conditional.clinical_variables)
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203 #end if
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204 --top_features $plot.plot_cox_conditional.top_features
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205 --event_value $plot.plot_cox_conditional.event_value
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206 #if str($plot.plot_cox_conditional.crossval_conditional.crossval) == 'yes':
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207 --crossval
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208 #end if
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209 #if str($plot.plot_cox_conditional.crossval_conditional.crossval) == 'yes':
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210 --n_splits $plot.plot_cox_conditional.crossval_conditional.n_splits
0
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211 #end if
3
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212 --random_state 42
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213 --output_dir plots
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214 --format $plot.plot_cox_conditional.format
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215 --dpi $plot.plot_cox_conditional.dpi
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216 #end if
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217 #end if
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218 #if str($plot.plot_scatter_conditional.plot_scatter) == 'yes':
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219 && python $__tool_directory__/flexynesis_plot.py
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220 --plot_type scatter
5
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221 --labels output/job.predicted_labels.tabular
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222 #if str($training_type.model) == 's_train':
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223 #if len($targets) > 0 or (str($surv_event_var) != 'None' and str($surv_time_var) != 'None'):
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224 --target_value \$target_value
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225 #end if
3
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226 #end if
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227 --output_dir plots
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228 --format $plot.plot_scatter_conditional.format
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229 --dpi $plot.plot_scatter_conditional.dpi
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230 #end if
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231 #if str($plot.plot_concordance_conditional.plot_concordance) == 'yes':
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232 && python $__tool_directory__/flexynesis_plot.py
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233 --plot_type concordance_heatmap
5
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234 --labels output/job.predicted_labels.tabular
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235 #if str($training_type.model) == 's_train':
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236 #if len($targets) > 0 or (str($surv_event_var) != 'None' and str($surv_time_var) != 'None'):
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237 --target_value \$target_value
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238 #end if
3
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239 #end if
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240 --output_dir plots
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241 --format $plot.plot_concordance_conditional.format
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242 --dpi $plot.plot_concordance_conditional.dpi
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243 #end if
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244 #if str($plot.plot_pr_curves_conditional.plot_pr_curves) == 'yes':
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245 && python $__tool_directory__/flexynesis_plot.py
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246 --plot_type pr_curve
5
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247 --labels output/job.predicted_labels.tabular
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248 #if str($training_type.model) == 's_train':
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249 #if len($targets) > 0 or (str($surv_event_var) != 'None' and str($surv_time_var) != 'None'):
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250 --target_value \$target_value
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251 #end if
3
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252 #end if
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253 --output_dir plots
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254 --format $plot.plot_pr_curves_conditional.format
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255 --dpi $plot.plot_pr_curves_conditional.dpi
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256 #end if
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257 #if str($plot.plot_roc_curves_conditional.plot_roc_curves) == 'yes':
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258 && python $__tool_directory__/flexynesis_plot.py
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259 --plot_type roc_curve
5
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260 --labels output/job.predicted_labels.tabular
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261 #if str($training_type.model) == 's_train':
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262 #if len($targets) > 0 or (str($surv_event_var) != 'None' and str($surv_time_var) != 'None'):
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263 --target_value \$target_value
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264 #end if
3
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265 #end if
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266 --output_dir plots
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267 --format $plot.plot_roc_curves_conditional.format
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268 --dpi $plot.plot_roc_curves_conditional.dpi
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269 #end if
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270 #if str($plot.plot_boxplot_conditional.plot_boxplot) == 'yes':
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271 && python $__tool_directory__/flexynesis_plot.py
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272 --plot_type box_plot
5
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273 --labels output/job.predicted_labels.tabular
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274 #if str($training_type.model) == 's_train':
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275 #if len($targets) > 0 or (str($surv_event_var) != 'None' and str($surv_time_var) != 'None'):
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276 --target_value \$target_value
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277 #end if
3
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278 #end if
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279 --output_dir plots
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280 --format $plot.plot_boxplot_conditional.format
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281 --dpi $plot.plot_boxplot_conditional.dpi
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282 #end if
0
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283 ]]></command>
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284 <inputs>
3
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285 <expand macro="commercial_use_param"/>
0
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286 <conditional name="training_type">
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287 <param name="model" type="select" label="Type of Analysis" >
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288 <option value="s_train">Supervised training</option>
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289 <option value="us_train">Unsupervised Training</option>
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290 <option value="cm_train">Cross-modality Training</option>
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291 </param>
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292 <when value="s_train">
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293 <expand macro="main_inputs"/>
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294 <repeat name="omics" min="0" title="Multiple omics layers?">
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295 <expand macro="extra_inputs"/>
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296 </repeat>
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297 <conditional name="model_class" label="Model class">
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298 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
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299 <option value="DirectPred">DirectPred</option>
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300 <option value="GNN">GNN</option>
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301 <option value="MultiTripletNetwork">MultiTripletNetwork</option>
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302 <option value="RandomForest">RandomForest</option>
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303 <option value="SVM">SVM</option>
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304 <option value="RandomSurvivalForest">RandomSurvivalForest</option>
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305 <option value="XGBoost">XGBoost</option>
0
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306 </param>
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307 <when value="DirectPred"/>
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308 <when value="GNN">
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309 <param argument="--gnn_conv_type" type="select" label="Which graph convolution type to use.">
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310 <option value="GC">GC</option>
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311 <option value="GCN">GCN</option>
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312 <option value="SAGE">SAGE</option>
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313 </param>
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314 <param argument="--string_organism" type="select" label="STRING DB organism">
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315 <option value="9606">Homo sapiens</option>
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316 <option value="10090">Mus musculus</option>
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317 <option value="10116">Rattus norvegicus</option>
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318 <option value="9544">Macaca mulatta</option>
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319 </param>
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320 <param argument="--string_node_name" type="select" label="String node name" >
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321 <option value="gene_name">Gene name</option>
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322 <option value="gene_id">Gene id</option>
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323 </param>
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324 </when>
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325 <when value="MultiTripletNetwork"/>
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326 <when value="RandomForest"/>
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327 <when value="SVM"/>
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328 <when value="RandomSurvivalForest"/>
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329 <when value="XGBoost"/>
0
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330 </conditional>
5
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331 <repeat name="targets" min="0" title="Target variables">
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332 <param argument="--target_variables" type="data_column" data_ref="train_clin" optional="false" label="Column name in the train clinical data to use for predictions, multiple targets are allowed"/>
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333 </repeat>
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334 <param argument="--surv_event_var" type="data_column" data_ref="train_clin" optional="true" label="Column name in the train clinical data to use as survival event"/>
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335 <param argument="--surv_time_var" type="data_column" data_ref="train_clin" optional="true" label="Column name in the train clinical data to use as survival time"/>
0
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336 <expand macro="advanced"/>
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337 </when>
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338 <when value="us_train">
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339 <expand macro="main_inputs"/>
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340 <repeat name="omics" min="0" title="Multiple omics layers?">
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341 <expand macro="extra_inputs"/>
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342 </repeat>
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343 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
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344 <option value="supervised_vae">supervised_vae</option>
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345 </param>
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346 <expand macro="advanced"/>
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347 </when>
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348 <when value="cm_train">
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349 <expand macro="main_inputs"/>
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350 <param name="layer_main" type="select" label="Use this omics data as input or output layer?">
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351 <option value="input">Input</option>
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352 <option value="output">output</option>
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353 </param>
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354 <repeat name="omics" min="0" title="Multiple omics layers?">
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355 <expand macro="extra_inputs"/>
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356 <param name="layer" type="select" label="Use this omics data as input or output layer?">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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357 <option value="input">Input</option>
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358 <option value="output">output</option>
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359 </param>
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diff changeset
360 </repeat>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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361 <param argument="--model_class" type="select" label="Model class" help="The kind of model class to instantiate">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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362 <option value="CrossModalPred">CrossModalPred</option>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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363 </param>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
364 <expand macro="advanced"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
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365 </when>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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366 </conditional>
3
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367 <section name="plot" title="Visualization">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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368 <conditional name="plot_embeddings_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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369 <param name="plot_embeddings" type="select" label="Generate embeddings plot?" help="Generate PCA or UMAP plot of the test dataset">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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370 <option value="yes">Yes</option>
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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371 <option value="no" selected="true">No</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
372 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
373 <when value="no">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
374 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
375 <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
376 <param name="method" type="select" label="Transformation method">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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377 <option value="pca" selected="true">PCA</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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378 <option value="umap">UMAP</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
379 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
380 <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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parents: 1
diff changeset
381 </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
382 </conditional>
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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383 <conditional name="plot_km_conditional">
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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384 <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">
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>
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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386 <option value="no" selected="true">No</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
387 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
388 <when value="no">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
389 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
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 <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.">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
392 <expand macro="sanitizer_printable"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
393 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
394 <expand macro="plots_common_param"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
395 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
396 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
397 <conditional name="plot_cox_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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398 <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.">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
399 <option value="yes">Yes</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
400 <option value="no" selected="true">No</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
401 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
402 <when value="no">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
403 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
404 <when value="yes">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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405 <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.">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
406 <expand macro="sanitizer_printable"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
407 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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408 <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, ...).">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
409 <expand macro="sanitizer_printable"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
410 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
411 <param argument="--top_features" type="integer" min="1" value="20" label="Number of top important features to include in Cox model"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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412 <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.">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
413 <expand macro="sanitizer_printable"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
414 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
415 <conditional name="crossval_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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416 <param name="crossval" type="select" label="Performs K-fold cross-validation?">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
417 <option value="yes">Yes</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
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418 <option value="no" selected="true">No</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
419 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
420 <when value="yes">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
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421 <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
bgruening
parents: 1
diff changeset
422 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
423 <when value="no"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
424 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
425 <expand macro="plots_common_param"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
426 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
427 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
428 <conditional name="plot_scatter_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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429 <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
bgruening
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diff changeset
430 <option value="yes">Yes</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
431 <option value="no" selected="true">No</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
432 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
433 <when value="no">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
434 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
435 <when value="yes">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
436 <expand macro="plots_common_param"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
437 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
438 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
439 <conditional name="plot_concordance_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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440 <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
bgruening
parents: 1
diff changeset
441 <option value="yes">Yes</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
442 <option value="no" selected="true">No</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
443 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
444 <when value="no">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
445 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
446 <when value="yes">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
447 <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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448 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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449 </conditional>
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450 <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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451 <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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452 <option value="yes">Yes</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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453 <option value="no" selected="true">No</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
454 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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455 <when value="no">
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456 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
457 <when value="yes">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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diff changeset
458 <expand macro="plots_common_param"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
459 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
460 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
461 <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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462 <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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463 <option value="yes">Yes</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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464 <option value="no" selected="true">No</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
465 </param>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
466 <when value="no">
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467 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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468 <when value="yes">
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diff changeset
469 <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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470 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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471 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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472 <conditional name="plot_boxplot_conditional">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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473 <param name="plot_boxplot" type="select" label="Generate boxplot?" help="Generates a boxplot for all available targets.">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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474 <option value="yes">Yes</option>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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475 <option value="no" selected="true">No</option>
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476 </param>
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diff changeset
477 <when value="no">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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478 </when>
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diff changeset
479 <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
480 <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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481 </when>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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482 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
483 </section>
0
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484 </inputs>
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485 <outputs>
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486 <collection name="results" type="list" label="${tool.name} on ${on_string}: results">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
487 <discover_datasets pattern="(?P&lt;name&gt;.+)\.tabular$" format="tabular" directory="output"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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488 </collection>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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489 <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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490 <discover_datasets pattern="__name_and_ext__" directory="plots"/>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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491 <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>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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492 </collection>
0
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493 </outputs>
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diff changeset
494 <tests>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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495 <!-- test 1: Supervised training with GEX and CNV data, DirectPred model, Erlotinib target -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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496 <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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497 <param name="non_commercial_use" value="True"/>
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diff changeset
498 <conditional name="training_type">
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499 <param name="model" value="s_train"/>
5
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500 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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501 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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502 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
503 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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504 <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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505 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
506 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
507 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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508 <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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509 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
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diff changeset
510 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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511 <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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512 </conditional>
5
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diff changeset
513 <repeat name="targets">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
514 <param name="target_variables" value="3"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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515 </repeat>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
516 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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517 <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
518 </section>
0
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519 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
520 <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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521 <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
522 <assert_contents>
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523 <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
524 </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
525 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
526 <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
527 <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
528 <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
529 </assert_contents>
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diff changeset
530 </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
531 <element name="job.feature_importance.GradientShap">
0
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532 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
533 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
534 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
535 <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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diff changeset
536 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
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537 </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
538 <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
539 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
540 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
541 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
542 <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
543 </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
544 </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
545 <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
546 <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
547 <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
548 </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
549 </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
550 <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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diff changeset
551 <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
552 <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
553 </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
554 </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
555 <element name="job.predicted_labels">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
556 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
557 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
558 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
559 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
560 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
561 <element name="job.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
562 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
563 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
564 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
565 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
566 </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
567 </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
568 </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
569 </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
570 <!-- test 2: Supervised training with GEX data, DirectPred model, Erlotinib target -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
571 <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
572 <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
573 <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
574 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
575 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
576 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
577 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
578 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
579 <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
580 <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
581 <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
582 </conditional>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
583 <repeat name="targets">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
584 <param name="target_variables" value="3"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
585 </repeat>
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
586 <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
587 <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
588 </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
589 </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
590 <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
591 <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
592 <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
593 <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
594 </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
595 </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
596 <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
597 <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
598 <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
599 </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
600 </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
601 <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
602 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
603 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
604 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
605 <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
606 </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
607 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
608 <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
609 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
610 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
611 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
612 <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
613 </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
614 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
615 <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
616 <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
617 <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
618 </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
619 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
620 <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
621 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
622 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
623 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
624 </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
625 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
626 <element name="job.stats">
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627 <assert_contents>
5
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628 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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629 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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630 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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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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diff changeset
633 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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634 </test>
3
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diff changeset
635 <!-- test 3: Supervised training with GEX and CNV data, DirectPred model, Irinotecan target -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
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636 <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
637 <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
638 <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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639 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
640 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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641 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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642 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
643 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
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parents: 0
diff changeset
644 <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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645 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
646 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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647 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
648 <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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649 </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
650 <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
651 <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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652 </conditional>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
653 <repeat name="targets">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
654 <param name="target_variables" value="4"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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655 </repeat>
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
656 <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
657 <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
658 </section>
0
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659 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
660 <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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661 <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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662 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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663 <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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664 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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665 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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666 <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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667 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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668 <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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669 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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670 </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
671 <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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672 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
673 <has_text_matching expression="Irinotecan\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
674 <has_text_matching expression="Irinotecan\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
675 <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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diff changeset
676 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
677 </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
678 <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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diff changeset
679 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
680 <has_text_matching expression="Irinotecan\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
681 <has_text_matching expression="Irinotecan\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
682 <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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683 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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684 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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685 <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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686 <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
687 <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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688 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
689 </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
690 <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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691 <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
692 <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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693 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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694 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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695 <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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696 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
697 <has_text_matching expression="source_dataset:A-704\tIrinotecan\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
698 <has_text_matching expression="target_dataset:KMRC-20\tIrinotecan\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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699 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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700 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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701 <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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702 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
703 <has_text_matching expression="DirectPred\tIrinotecan\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
704 <has_text_matching expression="DirectPred\tIrinotecan\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
705 <has_text_matching expression="DirectPred\tIrinotecan\tnumerical\tpearson_corr\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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706 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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707 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
708 </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
709 </test>
3
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diff changeset
710 <!-- 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
711 <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
712 <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
713 <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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714 <param name="model" value="us_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
715 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
716 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
717 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
718 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
719 <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
720 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
721 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
722 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
723 <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
724 </repeat>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
725 <param name="model_class" value="supervised_vae"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
726 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
727 <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
728 </section>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
729 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
730 <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
731 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
732 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
733 <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
734 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
735 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
736 <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
737 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
738 <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
739 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
740 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
741 <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
742 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
743 <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
744 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
745 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
746 <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
747 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
748 <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
749 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
750 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
751 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
752 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
753 <!-- test 5: Cross-modality training with GEX and CNV data, CrossModalPred model -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
754 <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
755 <param name="non_commercial_use" value="True"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
756 <conditional name="training_type">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
757 <param name="model" value="cm_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
758 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
759 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
760 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
761 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
762 <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
763 <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
764 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
765 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
766 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
767 <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
768 <param name="layer" value="output"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
769 </repeat>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
770 <param name="model_class" value="CrossModalPred"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
771 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
772 <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
773 </section>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
774 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
775 <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
776 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
777 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
778 <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
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 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
781 <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
782 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
783 <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
784 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
785 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
786 <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
787 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
788 <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
789 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
790 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
791 <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
792 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
793 <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
794 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
795 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
796 <element name="job.test_decoded.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
797 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
798 <has_n_lines n="23"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
799 </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
800 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
801 <element name="job.train_decoded.omics_foo">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
802 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
803 <has_n_lines n="23"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
804 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
805 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
806 </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
807 </test>
3
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parents: 1
diff changeset
808 <!-- 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
809 <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
810 <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
811 <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
812 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
813 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
814 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
815 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
816 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
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parents: 0
diff changeset
817 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
818 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
819 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
820 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
821 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
822 </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
823 <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
824 <param name="model_class" value="GNN"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
825 <param name="gnn_conv_type" value="GC"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
826 <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
827 <param name="string_node_name" value="gene_name"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
828 </conditional>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
829 <repeat name="targets">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
830 <param name="target_variables" value="3"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
831 </repeat>
1
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parents: 0
diff changeset
832 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
833 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
834 </section>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
835 </conditional>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
836 <output_collection name="results" type="list">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
837 <element name="job.embeddings_test">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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838 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
839 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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840 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
841 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
842 <element name="job.embeddings_train">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
843 <assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
844 <has_n_lines n="50"/>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
845 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
846 </element>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
847 <element name="job.feature_importance.GradientShap">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
848 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
849 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
850 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
851 <has_text_matching expression="GradientShap"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
852 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
853 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
854 <element name="job.feature_importance.IntegratedGradients">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
855 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
856 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
857 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
858 <has_text_matching expression="IntegratedGradients"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
859 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
860 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
861 <element name="job.feature_logs.bar">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
862 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
863 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
864 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
865 </element>
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parents: 0
diff changeset
866 <element name="job.feature_logs.omics_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
867 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
868 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
869 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
870 </element>
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parents: 0
diff changeset
871 <element name="job.predicted_labels">
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872 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
873 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
874 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
1
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875 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
876 </element>
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diff changeset
877 <element name="job.stats">
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diff changeset
878 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
879 <has_text_matching expression="GNN\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
880 <has_text_matching expression="GNN\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
881 <has_text_matching expression="GNN\tErlotinib\tnumerical\tpearson_corr\t"/>
1
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diff changeset
882 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
883 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
884 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
885 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
886 <!-- test 7: test 4 + checking whitespace in assay name -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
887 <test expect_num_outputs="1">
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
888 <param name="non_commercial_use" value="True"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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diff changeset
889 <conditional name="training_type">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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890 <param name="model" value="us_train"/>
5
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diff changeset
891 <param name="train_clin" value="train/clin" ftype="tabular"/>
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diff changeset
892 <param name="test_clin" value="test/clin" ftype="tabular"/>
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diff changeset
893 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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diff changeset
894 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
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parents: 0
diff changeset
895 <param name="assay_main" value="b ar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
896 <repeat name="omics">
5
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parents: 4
diff changeset
897 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
898 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
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bgruening
parents: 0
diff changeset
899 <param name="assay" value="f oo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
900 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
901 <param name="model_class" value="supervised_vae"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
902 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
903 <param name="hpo_iter" value="1"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
904 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
905 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
906 <output_collection name="results" type="list">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
907 <element name="job.embeddings_test">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
908 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
909 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
910 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
911 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
912 <element name="job.embeddings_train">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
913 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
914 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
915 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
916 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
917 <element name="job.feature_logs.b_ar">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
918 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
919 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
920 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
921 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
922 <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
923 <assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
924 <has_n_lines n="25"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
925 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
926 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
927 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
928 </test>
3
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parents: 1
diff changeset
929 <!-- test 8: Supervised training with GEX and CNV data, XGBoost model, Erlotinib target -->
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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parents: 1
diff changeset
930 <test expect_num_outputs="1">
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
931 <param name="non_commercial_use" value="True"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
932 <conditional name="training_type">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
933 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
934 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
935 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
936 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
937 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
938 <param name="assay_main" value="bar"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
939 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
940 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
941 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
942 <param name="assay" value="foo"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
943 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
944 <conditional name="model_class">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
945 <param name="model_class" value="XGBoost"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
946 </conditional>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
947 <repeat name="targets">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
948 <param name="target_variables" value="3"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
949 </repeat>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
950 <section name="advanced">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
951 <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
952 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
953 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
954 <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
955 <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
956 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
957 <has_text_matching expression="XGBoostRegressor\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
958 <has_text_matching expression="XGBoostRegressor\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
959 <has_text_matching expression="XGBoostRegressor\tErlotinib\tnumerical\tpearson_corr\t"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
960 </assert_contents>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
961 </element>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
962 </output_collection>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
963 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
964 <!-- 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
965 <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
966 <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
967 <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
968 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
969 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
970 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
971 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
972 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
973 <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
974 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
975 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
976 <param name="test_omics" value="test/cnv" ftype="tabular"/>
1
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
977 <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
978 </repeat>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
979 <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
980 <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
981 </conditional>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
982 <repeat name="targets">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
983 <param name="target_variables" value="3"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
984 </repeat>
1
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parents: 0
diff changeset
985 <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
986 <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
987 <param name="feature_importance_method" value="IntegratedGradients"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
988 <param name="val_size" value="0.2"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
989 </section>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
990 </conditional>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
bgruening
parents: 0
diff changeset
991 <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
992 <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
993 <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
994 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
995 </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
996 </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
997 <element name="job.embeddings_train">
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
998 <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
999 <has_n_lines n="50"/>
b353dad17ab7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 973836fb40ecb9c0ac26f675d12b20fc8e5f51f4
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parents: 0
diff changeset
1000 </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
1001 </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
1002 <element name="job.feature_importance.IntegratedGradients">
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1003 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
1004 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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parents: 4
diff changeset
1005 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1006 </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
1007 </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
1008 <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
1009 <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
1010 <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
1011 </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
1012 </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
1013 <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
1014 <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
1015 <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
1016 </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
1017 </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
1018 <element name="job.predicted_labels">
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1019 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1020 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1021 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1022 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1023 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1024 <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
1025 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1026 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1027 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1028 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1029 </assert_contents>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1030 </element>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1031 </output_collection>
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1032 </test>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1033 <!-- 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
1034 <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
1035 <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
1036 <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
1037 <param name="model" value="s_train"/>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1038 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1039 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1040 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1041 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1042 <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
1043 <repeat name="omics">
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1044 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1045 <param name="test_omics" value="test/cnv" ftype="tabular"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1046 <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
1047 </repeat>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1048 <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
1049 <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
1050 </conditional>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1051 <repeat name="targets">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1052 <param name="target_variables" value="3"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1053 </repeat>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1054 <section name="advanced">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1055 <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
1056 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1057 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1058 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1059 <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
1060 <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
1061 <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
1062 <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
1063 <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
1064 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1065 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1066 <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
1067 <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
1068 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1069 <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
1070 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1071 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1072 <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
1073 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1074 <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
1075 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1076 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1077 <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
1078 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1079 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1080 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1081 <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
1082 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1083 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1084 <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
1085 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1086 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1087 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1088 <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
1089 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1090 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1091 <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
1092 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1093 <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
1094 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1095 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1096 <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
1097 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1098 <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
1099 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1100 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1101 <element name="job.predicted_labels">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1102 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1103 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1104 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1105 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1106 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1107 <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
1108 <assert_contents>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1109 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1110 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1111 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1112 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1113 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1114 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1115 <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
1116 <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
1117 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1118 <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
1119 <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
1120 <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
1121 <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
1122 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1123 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1124 <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
1125 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1126 <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
1127 <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
1128 <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
1129 <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
1130 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1131 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1132 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1133 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1134 <!-- 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
1135 <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
1136 <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
1137 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1138 <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
1139 <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
1140 <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
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="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
1148 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1149 <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
1150 <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
1151 <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
1152 <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
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 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1156 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1157 <!-- 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
1158 <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
1159 <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
1160 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1161 <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
1162 <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
1163 <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
1164 <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
1165 <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
1166 <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
1167 <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
1168 <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
1169 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1170 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1171 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1172 <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
1173 <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
1174 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1175 <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
1176 <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
1177 <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
1178 <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
1179 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1180 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1181 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1182 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1183 <!-- 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
1184 <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
1185 <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
1186 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1187 <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
1188 <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
1189 <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
1190 <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
1191 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1192 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1193 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1194 <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
1195 <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
1196 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1197 <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
1198 <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
1199 <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
1200 <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
1201 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1202 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1203 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1204 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1205 <!-- 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
1206 <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
1207 <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
1208 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1209 <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
1210 <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
1211 <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
1212 <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
1213 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1214 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1215 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1216 <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
1217 <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
1218 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1219 <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
1220 <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
1221 <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
1222 <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
1223 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1224 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1225 <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
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 <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
1228 <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
1229 <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
1230 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1231 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1232 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1233 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1234 <!-- 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
1235 <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
1236 <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
1237 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1238 <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
1239 <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
1240 <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
1241 <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
1242 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1243 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1244 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1245 <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
1246 <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
1247 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1248 <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
1249 <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
1250 <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
1251 <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
1252 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1253 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1254 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1255 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1256 <!-- 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
1257 <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
1258 <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
1259 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1260 <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
1261 <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
1262 <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
1263 <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
1264 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1265 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1266 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1267 <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
1268 <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
1269 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1270 <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
1271 <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
1272 <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
1273 <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
1274 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1275 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1276 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1277 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1278 <!-- 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
1279 <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
1280 <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
1281 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1282 <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
1283 <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
1284 <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
1285 <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
1286 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1287 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1288 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1289 <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
1290 <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
1291 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1292 <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
1293 <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
1294 <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
1295 <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
1296 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1297 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1298 <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
1299 <assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1300 <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
1301 <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
1302 <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
1303 <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
1304 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1305 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1306 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1307 </test>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1308 <!-- 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
1309 <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
1310 <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
1311 <section name="plot">
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1312 <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
1313 <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
1314 <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
1315 <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
1316 <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
1317 <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
1318 <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
1319 <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
1320 <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
1321 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1322 <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
1323 <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
1324 </conditional>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1325 </section>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1326 </expand>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1327 <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
1328 <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
1329 <assert_contents>
4
1a5f8cedda43 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit d3154a8d94e936c33056665edc74d103e54fc981
bgruening
parents: 3
diff changeset
1330 <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
1331 <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
1332 <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
1333 <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
1334 </assert_contents>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1335 </element>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1336 </output_collection>
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1337 </test>
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1338 <!-- test 19: Supervised training with GEX and CNV data, DirectPred model, Erlotinib and Crizotinib targets -->
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1339 <test expect_num_outputs="1">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1340 <param name="non_commercial_use" value="True"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1341 <conditional name="training_type">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1342 <param name="model" value="s_train"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1343 <param name="train_clin" value="train/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1344 <param name="test_clin" value="test/clin" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1345 <param name="train_omics_main" value="train/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1346 <param name="test_omics_main" value="test/gex" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1347 <param name="assay_main" value="bar"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1348 <repeat name="omics">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1349 <param name="train_omics" value="train/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1350 <param name="test_omics" value="test/cnv" ftype="tabular"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1351 <param name="assay" value="foo"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1352 </repeat>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1353 <conditional name="model_class">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1354 <param name="model_class" value="DirectPred"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1355 </conditional>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1356 <repeat name="targets">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1357 <param name="target_variables" value="3"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1358 </repeat>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1359 <repeat name="targets">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1360 <param name="target_variables" value="2"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1361 </repeat>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1362 <section name="advanced">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1363 <param name="hpo_iter" value="1"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1364 </section>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1365 </conditional>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1366 <assert_stdout>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1367 <has_text_matching expression="Target variables: Erlotinib,Crizotinib"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1368 </assert_stdout>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1369 <output_collection name="results" type="list">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1370 <element name="job.embeddings_test">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1371 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1372 <has_n_lines n="50"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1373 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1374 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1375 <element name="job.embeddings_train">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1376 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1377 <has_n_lines n="50"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1378 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1379 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1380 <element name="job.feature_importance.GradientShap">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1381 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1382 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1383 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1384 <has_text_matching expression="Crizotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1385 <has_text_matching expression="Crizotinib\t0\t\tbar\tABCC4\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1386 <has_text_matching expression="GradientShap"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1387 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1388 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1389 <element name="job.feature_importance.IntegratedGradients">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1390 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1391 <has_text_matching expression="Erlotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1392 <has_text_matching expression="Erlotinib\t0\t\tbar\tABCC4\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1393 <has_text_matching expression="Crizotinib\t0\t\tbar\tA2M\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1394 <has_text_matching expression="Crizotinib\t0\t\tbar\tABCC4\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1395 <has_text_matching expression="IntegratedGradients"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1396 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1397 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1398 <element name="job.feature_logs.bar">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1399 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1400 <has_n_lines n="25"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1401 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1402 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1403 <element name="job.feature_logs.omics_foo">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1404 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1405 <has_n_lines n="25"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1406 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1407 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1408 <element name="job.predicted_labels">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1409 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1410 <has_text_matching expression="source_dataset:A-704\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1411 <has_text_matching expression="source_dataset:A-704\tCrizotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1412 <has_text_matching expression="target_dataset:KMRC-20\tErlotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1413 <has_text_matching expression="target_dataset:KMRC-20\tCrizotinib\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1414 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1415 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1416 <element name="job.stats">
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1417 <assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1418 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1419 <has_text_matching expression="DirectPred\tCrizotinib\tnumerical\tmse\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1420 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1421 <has_text_matching expression="DirectPred\tCrizotinib\tnumerical\tr2\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1422 <has_text_matching expression="DirectPred\tErlotinib\tnumerical\tpearson_corr\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1423 <has_text_matching expression="DirectPred\tCrizotinib\tnumerical\tpearson_corr\t"/>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1424 </assert_contents>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1425 </element>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1426 </output_collection>
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1427 </test>
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1428 </tests>
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1429 <help><![CDATA[
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1430 @COMMON_HELP@
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1431
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1432 .. image:: https://raw.githubusercontent.com/BIMSBbioinfo/flexynesis/c4634d97f84e51f569dcfdab2caf42c9be453ef6/img/graphical_abstract.jpg
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1433 :width: 600
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1434
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1435 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1436
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1437 **Input Files**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1438
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1439 **clin.tabular**
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1440
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1441 clin.tabular contains the sample metadata. The first column contains unique sample identifiers. The other columns contain sample-associated clinical variables. NA values are allowed in the clinical variables.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1442
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1443 The format might look like so:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1444
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1445 ======== === === ===
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1446 , v1 v2 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1447 -------- --- --- ---
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1448 sample1 a b ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1449 -------- --- --- ---
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1450 sample2 c d ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1451 -------- --- --- ---
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1452 sample3 e f ...
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1453 -------- --- --- ---
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1454 ... ... ... ...
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1455 ======== === === ===
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1456
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1457 .
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1458
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1459 **omics.tabular**
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1460
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1461 The first column of the feature tables must be unique feature identifiers (e.g. gene names). The column names must be sample identifiers that should overlap with those in the clin.tabular. They don't have to be completely identical or in the same order. Samples from the clin.tabular that are not represented in the omics table will be dropped.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1462
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1463 The format might look like so:
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1464
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1465 ===== ======= ======= ======= =======
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1466 , sample1 sample2 sample3 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1467 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1468 gene1 0 1 2 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1469 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1470 gene2 3 3 5 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1471 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1472 gene3 2 3 4 ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1473 ----- ------- ------- ------- -------
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1474 ... ... ... ... ...
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1475 ===== ======= ======= ======= =======
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1476
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1477 .
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1478
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1479 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1480
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1481 **Concordance between train/test splits:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1482
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1483 The corresponding omics files in train/test splits must contain overlapping feature names (they don't have to be identical or in the same order). The clin.tabular files in train/test must contain matching clinical variables.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1484
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1485 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1486
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1487 **Supervised Training**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1488
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1489 **Minimum requirements**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1490
5
466b593fd87e planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 4
diff changeset
1491 * clin.tabular and omics.tabular files for training and testing
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1492 * Selection of a tool/model
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1493 * 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
bgruening
parents:
diff changeset
1494
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1495 Flexynesis supports both single-task and multi-task training. We can provide one or more target variables and optionally survival variables as input and Flexynesis will build the appropriate model architecture. If the selected variable is numerical, a Multi-Layered-Perceptron (MLP) with MSE loss will be used. If a categorical variable is provided, an MLP with cross-entropy-loss will be utilized. If survival variables are provided, an MLP with Cox-Proportional-Hazards loss will be attached to the model.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1496
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1497 **Regression:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1498
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1499
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1500 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
bgruening
parents:
diff changeset
1501
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1502 **Classification:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1503
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1504
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1505 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
bgruening
parents:
diff changeset
1506
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1507 **Survival Analysis:**
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
1508
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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parents:
diff changeset
1509
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1510 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
bgruening
parents: 1
diff changeset
1511 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
bgruening
parents:
diff changeset
1512
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1513 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1514
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents: 1
diff changeset
1515 **Note:** Flexynesis can be trained with multiple target variables, which can be a mixture of regression/classification/survival tasks.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1516
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1517 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
1518
3
525c661a7fdc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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diff changeset
1519 **Note:** For the supervised tasks, the user can easily switch between different model architectures.
0
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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diff changeset
1520
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1521 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
1522
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
1523 **Note:** If you choose **MultiTripletNetwork** model, the first target variable should be a categorical variable.
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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diff changeset
1524
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
parents:
diff changeset
1525 .. class:: infomark
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
bgruening
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1526
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1527 **Note:** If you choose **GNN** model, the features should have the same naming convention between different omics modalities.
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1528
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1529 .. class:: infomark
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1530
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1531 **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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1532
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1533 -----
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1534
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1535 **Unsupervised Training**
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1536
3
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1537 In the absence of any target variables or survival variables, you can use a VAE architecture to carry out unsupervised training.
0
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1538
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1539 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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1540
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1541 **Cross-modality Training**
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1542
3
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1543 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.
0
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1544
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1545 .. class:: infomark
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1546
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1547 **Note:** if you use same input and output layers, it will be the same as unsupervised training.
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1548
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1549 -----
98431bd19f18 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/flexynesis commit b6763da7273957b7362787b7fdc6af5572161adb
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1550
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1551 .. class:: infomark
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1552
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1553 **Modality fusion:**
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1554
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1555 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.
0
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1556
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1557 .. _Documentation: https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/site/
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1558 .. _copyright holders: https://github.com/BIMSBbioinfo/flexynesis
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1559 ]]></help>
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1560 <expand macro="creator"/>
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1561 <expand macro="citations"/>
0
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1562 </tool>