Mercurial > repos > bgruening > flexynesis_plot

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
author bgruening
date Wed, 23 Jul 2025 07:49:52 +0000
parents 3c5d82bf6e8a
children
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bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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1 <tool id="flexynesis_plot" name="Flexynesis plot" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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2 <description>tool for visualizing flexynesis results</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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6 <expand macro="requirements"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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7 <required_files>
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8 <include path="flexynesis_plot.py" />
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9 </required_files>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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10 <command detect_errors="exit_code"><![CDATA[
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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11 @CHECK_NON_COMMERCIAL_USE@
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12 mkdir -p inputs/ plots/ &&
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13 #if str($plot_conditional.plot_type) != 'cox_plot':
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14 ln -s '$plot_conditional.labels' inputs/labels.tabular &&
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15 #end if
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bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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16 #if $plot_conditional.plot_type == "dimred":
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17 ln -s '$plot_conditional.embeddings' inputs/embeddings.tabular &&
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18 #end if
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19 #if $plot_conditional.plot_type == "km_plot":
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20 ln -s '$plot_conditional.survival_data' inputs/survival_data.tabular &&
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21 survival_event=`'$__tool_directory__/index_to_name.py' inputs/survival_data.tabular $plot_conditional.surv_event_var` &&
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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22 ## check if survival variable is numerical
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23 echo "Survival event variable: \$survival_event" &&
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24 python '$__tool_directory__/flexynesis_utils.py' --util validate_survival --clin inputs/survival_data.tabular --clin_variable \$survival_event &&
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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25 survival_time=`'$__tool_directory__/index_to_name.py' inputs/survival_data.tabular $plot_conditional.surv_time_var` &&
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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26 echo "Survival time variable: \$survival_time" &&
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27 #end if
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28 #if $plot_conditional.plot_type == "cox_plot":
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29 ln -s '$plot_conditional.important_features' inputs/important_features.tabular &&
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30 ln -s '$plot_conditional.clinical_train' inputs/clinical_train.tabular &&
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31 ln -s '$plot_conditional.clinical_test' inputs/clinical_test.tabular &&
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32 ln -s '$plot_conditional.omics_train' inputs/omics_train.tabular &&
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33 ln -s '$plot_conditional.omics_test' inputs/omics_test.tabular &&
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34 survival_event=`'$__tool_directory__/index_to_name.py' inputs/clinical_train.tabular $plot_conditional.surv_event_var` &&
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35 ## check if survival variable is numerical
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36 echo "Survival event variable: \$survival_event" &&
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37 python '$__tool_directory__/flexynesis_utils.py' --util validate_survival --clin inputs/clinical_train.tabular --clin_variable \$survival_event &&
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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38 survival_time=`'$__tool_directory__/index_to_name.py' inputs/clinical_train.tabular $plot_conditional.surv_time_var` &&
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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39 echo "Survival time variable: \$survival_time" &&
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40 #if str($plot_conditional.clinical_variables) != 'None':
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41 covars=`'$__tool_directory__/index_to_name.py' inputs/clinical_train.tabular $plot_conditional.clinical_variables` &&
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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42 ## check if survival variable is numerical
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43 echo "Clinical variables: \$covars" &&
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44 python '$__tool_directory__/flexynesis_utils.py' --util validate_covariate --clin inputs/clinical_train.tabular --clin_variable \$covars &&
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45 #end if
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46 #end if
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47 #if $plot_conditional.plot_type == "dimred":
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48 ## set target variables
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49 color_col=`'$__tool_directory__/index_to_name.py' inputs/labels.tabular $plot_conditional.color` &&
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50 echo "Color: \$color_col" &&
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51 python '$__tool_directory__/flexynesis_plot.py'
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52 --plot_type dimred
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53 --embeddings inputs/embeddings.tabular
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54 --labels inputs/labels.tabular
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55 --method $plot_conditional.method
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56 --color \$color_col
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57 --output_dir plots
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58 --format $plot_conditional.format
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59 --dpi $plot_conditional.dpi
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60
3
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61 #else if $plot_conditional.plot_type == "scatter":
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62 #if $plot_conditional.true_label and $plot_conditional.predicted_label:
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63 true_label_col=`'$__tool_directory__/index_to_name.py' inputs/labels.tabular $plot_conditional.true_label` &&
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64 echo "True label: \$true_label_col" &&
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65 python '$__tool_directory__/flexynesis_utils.py' --util validate_covariate --clin inputs/labels.tabular --clin_variable \$true_label_col &&
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66
3
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67 predicted_label_col=`'$__tool_directory__/index_to_name.py' inputs/labels.tabular $plot_conditional.predicted_label` &&
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68 echo "Predicted label: \$predicted_label_col" &&
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69 python '$__tool_directory__/flexynesis_utils.py' --util validate_covariate --clin inputs/labels.tabular --clin_variable \$predicted_label_col &&
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70 #end if
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71 python '$__tool_directory__/flexynesis_plot.py'
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72 --plot_type scatter
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73 --labels inputs/labels.tabular
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74 #if $plot_conditional.true_label and $plot_conditional.predicted_label:
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75 --true_label \$true_label_col
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76 --predicted_label \$predicted_label_col
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77 #end if
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78 --output_dir plots
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79 --format $plot_conditional.format
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80 --dpi $plot_conditional.dpi
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81 #else if $plot_conditional.plot_type == "concordance_heatmap":
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82 #if $plot_conditional.true_label and $plot_conditional.predicted_label:
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83 true_label_col=`'$__tool_directory__/index_to_name.py' inputs/labels.tabular $plot_conditional.true_label` &&
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84 predicted_label_col=`'$__tool_directory__/index_to_name.py' inputs/labels.tabular $plot_conditional.predicted_label` &&
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85 echo "True label: \$true_label_col" &&
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86 echo "Predicted label: \$predicted_label_col" &&
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87 #end if
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88 python '$__tool_directory__/flexynesis_plot.py'
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89 --plot_type concordance_heatmap
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90 --labels inputs/labels.tabular
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91 #if $plot_conditional.true_label and $plot_conditional.predicted_label:
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92 --true_label \$true_label_col
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93 --predicted_label \$predicted_label_col
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94 #end if
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95 --output_dir plots
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96 --format $plot_conditional.format
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97 --dpi $plot_conditional.dpi
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98 #else if $plot_conditional.plot_type == "pr_curve":
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99 python '$__tool_directory__/flexynesis_plot.py'
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100 --plot_type pr_curve
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101 --labels inputs/labels.tabular
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102 --output_dir plots
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103 --format $plot_conditional.format
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104 --dpi $plot_conditional.dpi
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105 #else if $plot_conditional.plot_type == "roc_curve":
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106 python '$__tool_directory__/flexynesis_plot.py'
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107 --plot_type roc_curve
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108 --labels inputs/labels.tabular
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109 --output_dir plots
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110 --format $plot_conditional.format
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111 --dpi $plot_conditional.dpi
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112 #else if $plot_conditional.plot_type == "box_plot":
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113 python '$__tool_directory__/flexynesis_plot.py'
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114 --plot_type box_plot
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115 --labels inputs/labels.tabular
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116 --output_dir plots
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117 --format $plot_conditional.format
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118 --dpi $plot_conditional.dpi
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119 #else if $plot_conditional.plot_type == "km_plot":
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120 python '$__tool_directory__/flexynesis_plot.py'
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121 --plot_type kaplan_meier
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122 --labels inputs/labels.tabular
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123 --survival_data inputs/survival_data.tabular
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124 --surv_event_var \$survival_event
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125 --surv_time_var \$survival_time
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126 --output_dir plots
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127 --format $plot_conditional.format
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128 --dpi $plot_conditional.dpi
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129 #else if $plot_conditional.plot_type == "cox_plot":
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130 python '$__tool_directory__/flexynesis_plot.py'
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131 --plot_type cox
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132 --important_features inputs/important_features.tabular
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133 --clinical_train inputs/clinical_train.tabular
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134 --clinical_test inputs/clinical_test.tabular
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135 --omics_train inputs/omics_train.tabular
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136 --omics_test inputs/omics_test.tabular
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137 --layer '$plot_conditional.layer'
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138 --surv_time_var \$survival_time
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139 --surv_event_var \$survival_event
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140 #if str($plot_conditional.clinical_variables) != 'None':
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141 --clinical_variables \$covars
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142 #end if
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143 --top_features $plot_conditional.top_features
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144 #if str($plot_conditional.crossval_conditional.crossval) == 'yes':
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145 --crossval
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146 #end if
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147 #if str($plot_conditional.crossval_conditional.crossval) == 'yes':
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148 --n_splits $plot_conditional.crossval_conditional.n_splits
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149 #end if
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150 --random_state 42
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151 --output_dir plots
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152 --format $plot_conditional.format
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153 --dpi $plot_conditional.dpi
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154 #end if
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155 ]]></command>
0
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156 <inputs>
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157 <expand macro="commercial_use_param"/>
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158 <conditional name="plot_conditional">
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159 <param name="plot_type" type="select" label="Flexynesis plot">
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160 <option value="dimred">Dimensionality reduction</option>
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161 <option value="scatter">Scatter plot of known vs predicted labels</option>
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162 <option value="concordance_heatmap">Label concordance heatmap</option>
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163 <option value="pr_curve">Precision-recall curves</option>
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164 <option value="roc_curve">ROC curves</option>
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165 <option value="box_plot">Box plot</option>
3
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166 <option value="km_plot">Kaplan-Meier plot</option>
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167 <option value="cox_plot">Cox proportional hazards plot</option>
0
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168 </param>
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169 <when value="dimred">
3
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170 <expand macro="plots_common_param_svg">
0
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171 <expand macro="plots_common_input"/>
2
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172 <param argument="--embeddings" type="data" format="tabular" label="Embeddings" help="Generated by flexynesis"/>
3
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173 <param argument="--color" type="data_column" data_ref="labels" label="Column in the labels file to use for coloring the points in the plot"/>
0
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174 <param name="method" type="select" label="Transformation method">
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175 <option value="pca" selected="true">PCA</option>
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176 <option value="umap">UMAP</option>
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177 </param>
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178 </expand>
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179 </when>
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180 <when value="scatter">
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181 <expand macro="plots_common_param_svg">
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182 <expand macro="plots_common_input"/>
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183 <param argument="--true_label" type="data_column" data_ref="labels" optional="true" label="Column in the labels file to use for true labels"/>
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184 <param argument="--predicted_label" type="data_column" data_ref="labels" optional="true" label="Column in the labels file to use for predicted labels"/>
0
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185 </expand>
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186 </when>
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187 <when value="concordance_heatmap">
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188 <expand macro="plots_common_param_svg">
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189 <expand macro="plots_common_input"/>
3
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190 <param argument="--true_label" type="data_column" data_ref="labels" optional="true" label="Column in the labels file to use for true labels"/>
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191 <param argument="--predicted_label" type="data_column" data_ref="labels" optional="true" label="Column in the labels file to use for predicted labels"/>
0
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192 </expand>
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193 </when>
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194 <when value="pr_curve">
3
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195 <expand macro="plots_common_param_svg">
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196 <expand macro="plots_common_input"/>
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197 </expand>
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198 </when>
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199 <when value="roc_curve">
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200 <expand macro="plots_common_param_svg">
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201 <expand macro="plots_common_input"/>
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202 </expand>
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203 </when>
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204 <when value="box_plot">
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205 <expand macro="plots_common_param_svg">
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206 <expand macro="plots_common_input"/>
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207 </expand>
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208 </when>
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209 <when value="km_plot">
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210 <expand macro="plots_common_param_svg">
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211 <expand macro="plots_common_input"/>
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212 <param argument="--survival_data" type="data" format="tabular" label="Survival data"/>
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213 <param argument="--surv_event_var" type="data_column" data_ref="survival_data" label="Column in the survival data to use as survival event"/>
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214 <param argument="--surv_time_var" type="data_column" data_ref="survival_data" label="Column in the survival data to use as survival time"/>
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215 </expand>
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216 </when>
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217 <when value="cox_plot">
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218 <expand macro="plots_common_param_svg">
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219 <param argument="--important_features" type="data" format="tabular" label="Important features file"/>
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220 <param argument="--clinical_train" type="data" format="tabular" label="Clinical training data"/>
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221 <param argument="--clinical_test" type="data" format="tabular" label="Clinical test data"/>
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222 <param argument="--omics_train" type="data" format="tabular" label="Omics training data"/>
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223 <param argument="--omics_test" type="data" format="tabular" label="Omics test data"/>
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224 <param name="layer" type="text" optional="false" label="The class label to use from important features file" help="This corresponds to assay name in flexynesis tool.">
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225 <expand macro="sanitizer_letters"/>
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226 </param>
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227 <param argument="--surv_event_var" type="data_column" data_ref="clinical_train" label="Column in the clinical training data to use as survival event"/>
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228 <param argument="--surv_time_var" type="data_column" data_ref="clinical_train" label="Column in the clinical training data to use as survival time"/>
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229 <param argument="--clinical_variables" type="data_column" data_ref="clinical_train" optional="true" multiple="true" label="Columns in the train clinical data to use as clinical covariates and include in the Cox model (e.g SEX, AGE, ...), multiple covariates are allowed"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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230 <param argument="--top_features" type="integer" min="1" value="20" label="Number of top important features to include in Cox model"/>
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231 <conditional name="crossval_conditional">
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232 <param name="crossval" type="select" label="Performs K-fold cross-validation?">
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233 <option value="yes">Yes</option>
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234 <option value="no" selected="true">No</option>
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235 </param>
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236 <when value="yes">
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237 <param name="n_splits" type="integer" min="2" value="5" label="Number of folds for cross-validation"/>
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238 </when>
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239 <when value="no"/>
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240 </conditional>
0
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241 </expand>
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242 </when>
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243 </conditional>
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244 </inputs>
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245 <outputs>
3
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246 <collection name="plot_out" type="list" label="${tool.name} on ${on_string}: ${plot_conditional.plot_type} - ${plot_conditional.format}">
0
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247 <discover_datasets pattern="__name_and_ext__" directory="plots/"/>
3
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248 <filter>plot_conditional['format'] != 'svg'</filter>
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249 </collection>
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250 <!-- other types can be sniffed correctly by galaxy -->
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251 <collection name="plot_out_svg" format="svg" type="list" label="${tool.name} on ${on_string}: ${plot_conditional.plot_type} - svg">
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252 <discover_datasets pattern="__name_and_ext__" directory="plots/"/>
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253 <filter>plot_conditional['format'] == 'svg'</filter>
0
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254 </collection>
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255 </outputs>
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256 <tests>
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257 <!-- test 1: dimred -->
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258 <test expect_num_outputs="1">
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259 <param name="non_commercial_use" value="True"/>
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260 <conditional name="plot_conditional">
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261 <param name="plot_type" value="dimred"/>
2
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262 <param name="embeddings" value="embeddings.tabular"/>
3
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263 <param name="color" value="6"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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264 <param name="method" value="pca"/>
2
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265 <param name="labels" value="labels.tabular"/>
0
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266 <param name="format" value="jpg"/>
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267 <param name="dpi" value="300"/>
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268 </conditional>
3
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269 <output_collection name="plot_out" type="list" count="1">
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270 <element name="embeddings_pca_predicted_label">
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271 <assert_contents>
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272 <has_image_center_of_mass center_of_mass="970,731" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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273 <has_image_channels channels="3"/>
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274 <has_image_height height="1460" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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275 <has_image_width width="1940" delta="20"/>
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276 </assert_contents>
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277 </element>
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278 </output_collection>
0
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279 </test>
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280 <!-- test 2: scatter -->
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281 <test expect_num_outputs="1">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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282 <param name="non_commercial_use" value="True"/>
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283 <conditional name="plot_conditional">
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284 <param name="plot_type" value="scatter"/>
2
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285 <param name="labels" value="labels_scatter.tabular"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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286 <param name="format" value="jpg"/>
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287 <param name="dpi" value="300"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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288 </conditional>
3
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289 <output_collection name="plot_out" type="list" count="1">
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290 <element name="labels_scatter_CLAUDIN_SUBTYPE">
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291 <assert_contents>
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292 <has_image_center_of_mass center_of_mass="969,732" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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293 <has_image_channels channels="3"/>
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294 <has_image_height height="1460" delta="20"/>
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295 <has_image_width width="1941" delta="20"/>
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296 </assert_contents>
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297 </element>
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298 </output_collection>
0
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299 </test>
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300 <!-- test 3: concordance_heatmap -->
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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301 <test expect_num_outputs="1">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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302 <param name="non_commercial_use" value="True"/>
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303 <conditional name="plot_conditional">
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304 <param name="plot_type" value="concordance_heatmap"/>
2
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305 <param name="labels" value="labels.tabular"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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306 <param name="format" value="jpg"/>
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307 <param name="dpi" value="300"/>
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308 </conditional>
3
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309 <output_collection name="plot_out" type="list" count="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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310 <element name="labels_concordance_CLAUDIN_SUBTYPE">
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311 <assert_contents>
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312 <has_image_center_of_mass center_of_mass="1450,1306" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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313 <has_image_channels channels="3"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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314 <has_image_height height="2558" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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315 <has_image_width width="2768" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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316 </assert_contents>
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317 </element>
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318 </output_collection>
0
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319 </test>
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320 <!-- test 4: pr_curve -->
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321 <test expect_num_outputs="1">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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322 <param name="non_commercial_use" value="True"/>
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323 <conditional name="plot_conditional">
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324 <param name="plot_type" value="pr_curve"/>
2
3c5d82bf6e8a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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325 <param name="labels" value="labels_pr.tabular"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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326 <param name="format" value="jpg"/>
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327 <param name="dpi" value="300"/>
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328 </conditional>
3
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329 <output_collection name="plot_out" type="list" count="1">
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330 <element name="labels_pr_curves_CLAUDIN_SUBTYPE">
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331 <assert_contents>
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332 <has_image_center_of_mass center_of_mass="965,733" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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333 <has_image_channels channels="3"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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334 <has_image_height height="1461" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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335 <has_image_width width="1941" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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336 </assert_contents>
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337 </element>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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338 </output_collection>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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339 </test>
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340 <!-- test 5: roc_curve -->
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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341 <test expect_num_outputs="1">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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342 <param name="non_commercial_use" value="True"/>
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343 <conditional name="plot_conditional">
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344 <param name="plot_type" value="roc_curve"/>
2
3c5d82bf6e8a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
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345 <param name="labels" value="labels_pr.tabular"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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346 <param name="format" value="jpg"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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347 <param name="dpi" value="300"/>
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348 </conditional>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
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349 <output_collection name="plot_out" type="list" count="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
350 <element name="labels_roc_curves_CLAUDIN_SUBTYPE">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
351 <assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
352 <has_image_center_of_mass center_of_mass="971,732" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
353 <has_image_channels channels="3"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
354 <has_image_height height="1461" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
355 <has_image_width width="1941" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
356 </assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
357 </element>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
358 </output_collection>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
359 </test>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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diff changeset
360 <!-- test 6: box_plot -->
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
361 <test expect_num_outputs="1">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
362 <param name="non_commercial_use" value="True"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
363 <conditional name="plot_conditional">
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
364 <param name="plot_type" value="box_plot"/>
2
3c5d82bf6e8a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 1afbaf45449e25238935e222f983da62392c067a
bgruening
parents: 0
diff changeset
365 <param name="labels" value="labels_pr.tabular"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
366 <param name="format" value="jpg"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
367 <param name="dpi" value="300"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
368 </conditional>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
369 <output_collection name="plot_out" type="list" count="7">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
370 <element name="labels_box_plot_CLAUDIN_SUBTYPE_Basal">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
371 <assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
372 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
373 <has_image_channels channels="3"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
374 <has_image_height height="1766" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
375 <has_image_width width="2967" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
376 </assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
377 </element>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
378 <element name="labels_box_plot_CLAUDIN_SUBTYPE_Her2">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
379 <assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
380 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
381 <has_image_channels channels="3"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
382 <has_image_height height="1766" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
383 <has_image_width width="2967" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
384 </assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
385 </element>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
386 <element name="labels_box_plot_CLAUDIN_SUBTYPE_LumA">
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
387 <assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
388 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
389 <has_image_channels channels="3"/>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
390 <has_image_height height="1766" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
391 <has_image_width width="2967" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
392 </assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
393 </element>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
394 <element name="labels_box_plot_CLAUDIN_SUBTYPE_LumB">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
395 <assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
396 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
397 <has_image_channels channels="3"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
398 <has_image_height height="1766" delta="20"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
399 <has_image_width width="2967" delta="20"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
400 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
401 </element>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
402 <element name="labels_box_plot_CLAUDIN_SUBTYPE_NC">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
403 <assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
404 <has_image_center_of_mass center_of_mass="1485,875" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
405 <has_image_channels channels="3"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
406 <has_image_height height="1766" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
407 <has_image_width width="2967" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
408 </assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
409 </element>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
410 <element name="labels_box_plot_CLAUDIN_SUBTYPE_Normal">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
411 <assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
412 <has_image_center_of_mass center_of_mass="1485,878" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
413 <has_image_channels channels="3"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
414 <has_image_height height="1766" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
415 <has_image_width width="2967" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
416 </assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
417 </element>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
418 <element name="labels_box_plot_CLAUDIN_SUBTYPE_claudin-low">
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
419 <assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
420 <has_image_center_of_mass center_of_mass="1485,882" eps="20"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
421 <has_image_channels channels="3"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
422 <has_image_height height="1765" delta="20"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
423 <has_image_width width="2967" delta="20"/>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
424 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
425 </element>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
426 </output_collection>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
427 </test>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
428 <!-- test 7: dimred png-->
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
429 <test expect_num_outputs="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
430 <param name="non_commercial_use" value="True"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
431 <conditional name="plot_conditional">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
432 <param name="plot_type" value="dimred"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
433 <param name="embeddings" value="embeddings.tabular"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
434 <param name="color" value="6"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
435 <param name="method" value="pca"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
436 <param name="labels" value="labels.tabular"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
437 <param name="format" value="png"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
438 <param name="dpi" value="300"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
439 </conditional>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
440 <output_collection name="plot_out" type="list" count="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
441 <element name="embeddings_pca_predicted_label">
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
442 <assert_contents>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
443 <has_image_center_of_mass center_of_mass="970,730" eps="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
444 <has_image_channels channels="4"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
445 <has_image_height height="1461" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
446 <has_image_width width="1941" delta="20"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
447 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
448 </element>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
449 </output_collection>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
450 </test>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
451 <!-- test 8: roc_curve svg-->
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
452 <test expect_num_outputs="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
453 <param name="non_commercial_use" value="True"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
454 <conditional name="plot_conditional">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
455 <param name="plot_type" value="roc_curve"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
456 <param name="labels" value="labels_pr.tabular"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
457 <param name="format" value="svg"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
458 <param name="dpi" value="300"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
459 </conditional>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
460 <output_collection name="plot_out_svg" type="list" count="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
461 <element name="labels_roc_curves_CLAUDIN_SUBTYPE">
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
462 <assert_contents>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
463 <has_text_matching expression="ROC Curve"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
464 <has_text_matching expression="True Positive Rate"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
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465 </assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
466 </element>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
467 </output_collection>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
468 </test>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
469 <!-- test 9: km_plot -->
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
470 <test expect_num_outputs="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
471 <param name="non_commercial_use" value="True"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
472 <conditional name="plot_conditional">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
473 <param name="plot_type" value="km_plot"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
474 <param name="labels" value="labels_survival.tabular"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
475 <param name="survival_data" value="test/clin"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
476 <param name="surv_event_var" value="15"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
477 <param name="surv_time_var" value="14"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
478 <param name="format" value="jpg"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
479 <param name="dpi" value="300"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
480 </conditional>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
481 <output_collection name="plot_out" type="list" count="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
482 <element name="survival_data_km_km_risk_subtypes">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
483 <assert_contents>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
484 <has_image_center_of_mass center_of_mass="970,730" eps="20"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
485 <has_image_channels channels="3"/>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
486 <has_image_height height="1460" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
487 <has_image_width width="1940" delta="20"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
488 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
489 </element>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
490 </output_collection>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
491 </test>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
492 <!-- test 10: cox_plot -->
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
493 <test expect_num_outputs="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
494 <param name="non_commercial_use" value="True"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
495 <conditional name="plot_conditional">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
496 <param name="plot_type" value="cox_plot"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
497 <param name="important_features" value="feature_importance.tabular"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
498 <param name="clinical_train" value="train/clin"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
499 <param name="clinical_test" value="test/clin"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
500 <param name="omics_train" value="train/gex"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
501 <param name="omics_test" value="test/gex"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
502 <param name="layer" value="gex"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
503 <param name="surv_event_var" value="15"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
504 <param name="surv_time_var" value="14"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
505 <param name="clinical_variables" value="3,4"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
506 <param name="top_features" value="10"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
507 <param name="format" value="jpg"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
508 <param name="dpi" value="300"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
509 </conditional>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
510 <output_collection name="plot_out" type="list" count="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
511 <element name="important_features_cox_hazard_ratios">
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
512 <assert_contents>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
513 <has_image_center_of_mass center_of_mass="970,730" eps="20"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
514 <has_image_channels channels="3"/>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
515 <has_image_height height="1460" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
516 <has_image_width width="1940" delta="20"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
517 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
518 </element>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
519 </output_collection>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
520 </test>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
521 <!-- test 11: km_plot should fail because of non numeric target -->
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
522 <test expect_failure="true">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
523 <param name="non_commercial_use" value="True"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
524 <conditional name="plot_conditional">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
525 <param name="plot_type" value="km_plot"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
526 <param name="labels" value="labels_survival.tabular"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
527 <param name="survival_data" value="test/clin"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
528 <param name="surv_event_var" value="16"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
529 <param name="surv_time_var" value="14"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
530 <param name="format" value="jpg"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
531 <param name="dpi" value="300"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
532 </conditional>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
533 <assert_stderr>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
534 <has_text_matching expression="Error: Non-numeric values found in column 'class': Unable to parse string &quot;buz&quot; at position 0"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
535 </assert_stderr>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
536 </test>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
537 <!-- test 12: cox_plot should fail because of non numeric target -->
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
538 <test expect_failure="true">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
539 <param name="non_commercial_use" value="True"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
540 <conditional name="plot_conditional">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
541 <param name="plot_type" value="cox_plot"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
542 <param name="important_features" value="feature_importance.tabular"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
543 <param name="clinical_train" value="train/clin"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
544 <param name="clinical_test" value="test/clin"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
545 <param name="omics_train" value="train/gex"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
546 <param name="omics_test" value="test/gex"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
547 <param name="layer" value="gex"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
548 <param name="surv_event_var" value="15"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
549 <param name="surv_time_var" value="14"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
550 <param name="clinical_variables" value="3,4,16"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
551 <param name="top_features" value="10"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
552 <param name="format" value="jpg"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
553 <param name="dpi" value="300"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
554 </conditional>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
555 <assert_stderr>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
556 <has_text_matching expression="Error: Non-numeric values found in column 'class': Unable to parse string &quot;buz&quot; at position 0"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
557 </assert_stderr>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
558 </test>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
559 <!-- test 13: scatter unsupervised -->
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
560 <test expect_num_outputs="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
561 <param name="non_commercial_use" value="True"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
562 <conditional name="plot_conditional">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
563 <param name="plot_type" value="scatter"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
564 <param name="labels" value="non_flexy_label.tabular"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
565 <param name="true_label" value="11"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
566 <param name="predicted_label" value="12"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
567 <param name="format" value="jpg"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
568 <param name="dpi" value="300"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
569 </conditional>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
570 <output_collection name="plot_out" type="list" count="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
571 <element name="labels_scatter">
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
572 <assert_contents>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
573 <has_image_center_of_mass center_of_mass="970,730" eps="20"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
574 <has_image_channels channels="3"/>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
575 <has_image_height height="1460" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
576 <has_image_width width="1941" delta="20"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
577 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
578 </element>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
579 </output_collection>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
580 </test>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
581 <!-- test 14: concordance_heatmap unsupervised -->
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
582 <test expect_num_outputs="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
583 <param name="non_commercial_use" value="True"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
584 <conditional name="plot_conditional">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
585 <param name="plot_type" value="concordance_heatmap"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
586 <param name="labels" value="non_flexy_label.tabular"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
587 <param name="true_label" value="10"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
588 <param name="predicted_label" value="12"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
589 <param name="format" value="jpg"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
590 <param name="dpi" value="300"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
591 </conditional>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
592 <output_collection name="plot_out" type="list" count="1">
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
593 <element name="labels_concordance">
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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diff changeset
594 <assert_contents>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
595 <has_image_center_of_mass center_of_mass="1445,1306" eps="20"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
596 <has_image_channels channels="3"/>
3
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
597 <has_image_height height="2558" delta="20"/>
52b6f2ac38c7 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit 6b520305ec30e6dc37eba92c67a5368cea0fc5ad
bgruening
parents: 2
diff changeset
598 <has_image_width width="3051" delta="20"/>
0
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
599 </assert_contents>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
600 </element>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
601 </output_collection>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
602 </test>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
603 </tests>
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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diff changeset
604 <help><![CDATA[
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
605 @COMMON_HELP@
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
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diff changeset
606
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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diff changeset
607 Flexynesis plot is a comprehensive visualization tool designed to create various types of plots for analyzing machine learning results from the Flexynesis framework. This tool supports multiple visualization types to help researchers understand their data and model performance.
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
608
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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diff changeset
609 Available plot types include:
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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diff changeset
610
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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diff changeset
611 - **Dimensionality Reduction:** Visualizes high-dimensional data in a lower-dimensional space using methods like PCA or UMAP.
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
612 - **Scatter Plot:** Compares known and predicted labels to assess model performance.
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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diff changeset
613 - **Label Concordance Heatmap:** Displays the agreement between true and predicted labels in a heatmap format.
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
parents:
diff changeset
614 - **Precision-Recall Curves:** Plots precision against recall to evaluate the trade-off between these metrics.
bb91bf19eb40 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/flexynesis commit b2463fb68d0ae54864d87718ee72f5e063aa4587
bgruening
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615 - **ROC Curves:** Visualizes the true positive rate against the false positive rate to assess model discrimination.
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616 - **Box Plot:** Shows the distribution of predicted probabilities across different classes, highlighting medians and quartiles.
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617
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618
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619 **Input Files**
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620
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621 Main common input file is the labels file, which is the predicted labels file generated by Flexynesis. It should contain the following columns:
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622
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623 - `sample_id`: Unique identifier for each sample.
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624 - `variable`: The target variable used for the analysis.
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625 - `class_label`: The class labels for the samples, used in box plots.
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626 - `probability`: The predicted probabilities for the labels.
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627 - `known_label`: The true labels for the samples, used in scatter plots and concordance heatmaps.
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628 - `predicted_label`: The labels predicted by the Flexynesis model, used in scatter plots and concordance heatmaps.
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629
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630
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631 For dimensionality reduction plots, an additional embeddings file is required, which contains the reduced-dimensional representations of the samples. This file is generated by Flexynesis.
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632
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633
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634 .. class:: warningmark
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635
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636 PR and ROC curves can only be applied on classification tasks!
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637
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638
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639 .. _Documentation: https://bimsbstatic.mdc-berlin.de/akalin/buyar/flexynesis/site/
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640 .. _copyright holders: https://github.com/BIMSBbioinfo/flexynesis
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641 ]]></help>
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642 <expand macro="creator"/>
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643 <expand macro="citations"/>
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644 </tool>