Mercurial > repos > bgruening > ml_visualization_ex

annotate ml_visualization_ex.xml @ 9:72866f238ec4 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d970dae980fbe349414fc0889f719d875d999c5b"
author bgruening
date Fri, 27 Aug 2021 08:28:31 +0000
parents 8e7ae32df1ab
children 6c787aeeac06
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1 <tool id="ml_visualization_ex" name="Machine Learning Visualization Extension" version="@VERSION@" profile="20.05">
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2 <description>includes several types of plotting for machine learning</description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 <import>keras_macros.xml</import>
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6 </macros>
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7 <expand macro="python_requirements" />
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8 <expand macro="macro_stdio" />
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9 <version_command>echo "@VERSION@"</version_command>
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10 <command>
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11 <![CDATA[
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12 python '$__tool_directory__/ml_visualization_ex.py'
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13 --inputs '$inputs'
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14 #if $plotting_selection.plot_type in ['learning_curve', 'rfecv_gridscores']
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15 --infile1 '$plotting_selection.infile1'
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16 #elif $plotting_selection.plot_type in ['pr_curve', 'roc_curve']
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17 --infile1 '$plotting_selection.infile1'
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18 --infile2 '$plotting_selection.infile2'
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19 #elif $plotting_selection.plot_type == 'feature_importances'
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20 --estimator '$plotting_selection.infile_estimator'
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21 --infile1 '$plotting_selection.infile1'
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22 #elif $plotting_selection.plot_type == 'keras_plot_model'
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23 --model_config '$plotting_selection.infile_model_config'
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24 #elif $plotting_selection.plot_type == 'classification_confusion_matrix'
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25 --true_labels '$plotting_selection.infile_true'
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26 --predicted_labels '$plotting_selection.infile_predicted'
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27 --plot_color '$plotting_selection.plot_color'
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28 --title '$plotting_selection.title'
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29 #end if
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30 ]]>
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31 </command>
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32 <configfiles>
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33 <inputs name="inputs" />
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34 </configfiles>
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35 <inputs>
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36 <conditional name="plotting_selection">
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37 <param name="plot_type" type="select" label="Select a plotting type">
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38 <option value="learning_curve" selected="true">Learning curve</option>
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39 <option value="pr_curve">2-class / multpi-label Precison Recall curve</option>
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40 <option value="roc_curve">2-class / multi-label Receiver Operating Characteristic (ROC) curve</option>
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41 <option value="rfecv_gridscores">Number of features vs. Recursive Feature Elimination gridscores with corss-validation</option>
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42 <option value="feature_importances">Feature Importances plot</option>
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43 <option value="keras_plot_model">keras plot model - plot configuration of a neural network model</option>
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44 <option value="classification_confusion_matrix">Confusion matrix for classes</option>
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45 </param>
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46 <when value="learning_curve">
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47 <param name="infile1" type="data" format="tabular" label="Select the dataset containing values for plotting learning curve." help="This dataset should be the output of tool model_validation->learning_curve." />
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48 <param name="plot_std_err" type="boolean" truevalue="booltrue" falsevalue="boolfalse" optional="true" checked="false" label="Whether to plot standard error bar?" />
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49 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
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50 <param name="plot_format" type="select" label="The output format and library">
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51 <option value="html" selected="true">An interactive html by plotly</option>
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52 <!--<option value="png">PNG image by matplotlib</option> TODO-->
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53 </param>
0
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54 </when>
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55 <when value="pr_curve">
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56 <param name="infile1" type="data" format="tabular" label="Select the dataset containing true labels." help="y_true. Headered. For 2-class, single column contains both class labels (e.g. True and False). For multi-label, each column, hot-encoded, corresponds to one label." />
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57 <param name="infile2" type="data" format="tabular" label="Select the dataset containing predicted probabilities." help="y_preds. Headered. For 2-class, sinle column or the first column contains scores for the positive label. For multi-label, each column corresponds to one label." />
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58 <param name="pos_label" type="text" value="" optional="true" label="pos_label" help="The label of positive class. If not specified, it will be 1 by default." />
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59 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
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60 <param name="report_minimum_n_positives" type="integer" value="" optional="true" label="Report minimum number of positives" help="For mulitple label binary classifications, whose number of true postives is less than the threhold will be ignored." />
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61 <param name="plot_format" type="select" label="The output format and library">
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62 <option value="plotly_html" selected="true">An interactive html by plotly</option>
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63 <option value="matplotlib_svg">SVG image by matplotlib</option>
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64 </param>
0
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65 </when>
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66 <when value="roc_curve">
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67 <param name="infile1" type="data" format="tabular" label="Select the dataset containing true labels." help="y_true. Headered. For 2-class, single column contains both class labels (e.g. True and False). For multi-label, each column, hot-encoded, corresponds to one label." />
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68 <param name="infile2" type="data" format="tabular" label="Select the dataset containing predicted probabilities." help="y_preds. Headered. For 2-class, sinle column or the first column contains scores for the positive label. For multi-label, each column corresponds to one label." />
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69 <param name="pos_label" type="text" value="" optional="true" label="pos_label" help="The label of positive class. If not specified, it will be 1 by default." />
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70 <param name="drop_intermediate" type="boolean" truevalue="booltrue" falsevalue="boolfalse" optional="true" checked="true" label="drop_intermediate" help="Whether to drop some suboptimal thresholds which would not appear on a plotted ROC curve." />
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71 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
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72 <param name="report_minimum_n_positives" type="integer" value="" optional="true" label="Report minimum number of positives" help="For mulitple label binary classifications, whose number of true postives is less than the threhold will be ignored." />
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73 <param name="plot_format" type="select" label="The output format and library">
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74 <option value="plotly_html" selected="true">An interactive html by plotly</option>
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75 <option value="matplotlib_svg">SVG image by matplotlib</option>
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76 </param>
0
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77 </when>
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78 <when value="rfecv_gridscores">
7
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79 <param name="infile1" type="data" format="tabular" label="Select the dataset containing grid_scores from a fitted RFECV object." help="Headered. Single column. Could be Output from `estimator_attributes->grid_scores_`." />
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80 <param name="steps" type="text" value="" optional="true" label="Step IDs" help="List, containing hover labels for each grid_score. For example: `list(range(10)) + [15, 20]`." />
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81 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
4
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82 <param name="plot_format" type="select" label="The output format and library">
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83 <option value="html" selected="true">An interactive html by plotly</option>
1b2f7d4ee4e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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84 <!--<option value="png">PNG image by matplotlib</option> TODO-->
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85 </param>
0
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86 </when>
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87 <when value="feature_importances">
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88 <param name="infile_estimator" type="data" format="zip" label="Select the dataset containing fitted estimator/pipeline" />
7
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89 <param name="infile1" type="data" format="tabular" label="Select the dataset containing feature names" help="Make sure the headers (first row) are feature names." />
0
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90 <conditional name="column_selector_options">
7
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91 <expand macro="samples_column_selector_options" multiple="true" />
0
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92 </conditional>
7
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93 <param name="threshold" type="float" value="" optional="true" min="0." label="Threshold value" help="Features with importance below the threshold value will be ignored." />
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94 <param name="title" type="text" value="" optional="true" label="Custom plot title" help="Optional." />
4
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95 <param name="plot_format" type="select" label="The output format and library">
1b2f7d4ee4e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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96 <option value="html" selected="true">An interactive html by plotly</option>
1b2f7d4ee4e7 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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97 <!--<option value="png">PNG image by matplotlib</option> TODO-->
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98 </param>
0
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99 </when>
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100 <when value="keras_plot_model">
7
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101 <param name="infile_model_config" type="data" format="json" label="Select the JSON dataset containing configuration for a neural network model" />
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102 <param name="title" type="hidden" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
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103 <param name="plot_format" type="hidden" value="png" label="The output format and library" />
0
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104 </when>
7
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105
6
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106 <when value="classification_confusion_matrix">
7
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107 <param name="infile_true" type="data" format="tabular" label="Select dataset containing true labels" />
6
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108 <param name="header_true" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
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109 <conditional name="column_selector_options_true">
7
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110 <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile_true" />
6
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111 </conditional>
7
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112
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113 <param name="infile_predicted" type="data" format="tabular" label="Select dataset containing predicted labels" />
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114 <param name="header_predicted" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
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115 <param name="title" type="text" value="Confusion matrix between true and predicted labels" label="Plot title" />
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116 <param name="plot_format" type="hidden" value="png" label="The output format and library" />
6
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117 <param name="plot_color" type="select" label="Choose plot color">
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118 <option value="Greys">Greys</option>
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119 <option value="Purples">Purples</option>
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120 <option value="Blues">Blues</option>
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121 <option value="Greens" selected="true">Greens</option>
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122 <option value="Oranges">Oranges</option>
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123 <option value="Reds">Reds</option>
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124 <option value="Summer">Summer</option>
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125 <option value="Autumn">Autumn</option>
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126 <option value="RdYlGn">RdYlGn</option>
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127 <option value="Spectral">Spectral</option>
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128 <option value="winter">winter</option>
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129 </param>
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130 </when>
0
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131 </conditional>
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132 </inputs>
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133 <outputs>
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134 <data name="output" format="html" from_work_dir="output" label="${plotting_selection.plot_type} plot on ${on_string}">
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135 <change_format>
7
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136 <when input="plotting_selection.plot_format" value="png" format="png" />
0
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137 </change_format>
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138 </data>
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139 </outputs>
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140 <tests>
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141 <test>
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142 <param name="plot_type" value="roc_curve" />
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143 <param name="infile1" value="y_true.tabular" ftype="tabular" />
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144 <param name="infile2" value="y_score.tabular" ftype="tabular" />
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145 <output name="output" file="ml_vis04.html" compare="sim_size" />
0
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146 </test>
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147 <test>
7
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148 <param name="plot_type" value="feature_importances" />
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149 <param name="infile_estimator" value="best_estimator_.zip" ftype="zip" />
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150 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
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151 <param name="selected_column_selector_option" value="all_columns" />
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152 <output name="output" file="ml_vis01.html" compare="sim_size" />
0
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153 </test>
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154 <test>
7
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155 <param name="plot_type" value="learning_curve" />
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156 <param name="infile1" value="mv_result03.tabular" ftype="tabular" />
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157 <output name="output" file="ml_vis02.html" compare="sim_size" />
0
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158 </test>
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159 <test>
7
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160 <param name="plot_type" value="pr_curve" />
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161 <param name="infile1" value="y_true.tabular" ftype="tabular" />
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162 <param name="infile2" value="y_score.tabular" ftype="tabular" />
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163 <output name="output" file="ml_vis03.html" compare="sim_size" />
0
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164 </test>
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165 <test>
7
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166 <param name="plot_type" value="rfecv_gridscores" />
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167 <param name="infile1" value="grid_scores_.tabular" ftype="tabular" />
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168 <output name="output" file="ml_vis05.html" compare="sim_size" />
0
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169 </test>
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170 <test>
7
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171 <param name="plot_type" value="keras_plot_model" />
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172 <param name="infile_model_config" value="deepsear_1feature.json" ftype="json" />
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173 <output name="output" file="ml_vis05.png" compare="sim_size" delta="20000" />
0
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174 </test>
6
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175 <test>
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176 <param name="plot_type" value="classification_confusion_matrix" />
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177 <param name="infile_true" value="ml_confusion_true.tabular" ftype="tabular" />
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178 <param name="header_true" value="False" />
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179 <param name="selected_column_selector_option" value="all_columns" />
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180 <param name="infile_predicted" value="ml_confusion_predicted.tabular" ftype="tabular" />
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181 <param name="header_predicted" value="False" />
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182 <param name="title" value="Confusion matrix" />
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183 <param name="plot_color" value="winter" />
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184 <output name="output" file="ml_confusion_viz.png" compare="sim_size" />
6
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185 </test>
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186 <test>
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187 <param name="plot_type" value="classification_confusion_matrix" />
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188 <param name="infile_true" value="true_header.tabular" ftype="tabular" />
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189 <param name="header_true" value="True" />
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190 <param name="selected_column_selector_option" value="all_columns" />
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191 <param name="infile_predicted" value="predicted_header.tabular" ftype="tabular" />
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192 <param name="header_predicted" value="True" />
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193 <param name="title" value="Confusion matrix" />
6
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194 <param name="plot_color" value="winter" />
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195 <output name="output" file="ml_confusion_viz.png" compare="sim_size" />
6
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196 </test>
0
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197 </tests>
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198 <help>
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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199 <![CDATA[
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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200 **What it does**
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201 This tool ouputs serveral machine learning visualization plots using Plotly, including 'feature_importances', 'learning curve', 'precison recall curve', 'roc_curve', and 'number of featues vs. rfecv gridscores'. This tool also ouputs configuration diagram for a deep learning model using the Keras model JSON file as input.
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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202
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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203
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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204 **Feature importances**
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205
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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206 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/feature_importances.png
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207 :width: 400
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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208 :alt: feature importances
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209
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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210
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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211 **Learning curve**
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212
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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213 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/learning_curve.png
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214 :width: 400
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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215 :alt: learning curve
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216
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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217
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218 **Precison recall curve**
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219
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220 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/pr_curve.png
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221 :width: 400
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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222 :alt: precison recall curve
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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223
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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224
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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225 **Receiver operating characteristic curve**
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226
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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227 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/roc_curve.png
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228 :width: 400
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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229 :alt: Receiver operating characteristic curve
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230
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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231
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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232 **Number of featues vs. rfecv gridscores**
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233
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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234 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/rfecv_gridscore.png
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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235 :width: 400
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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236 :alt: Number of featues vs. rfecv gridscores
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237
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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238
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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239 **Deep learning model configuration**
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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240
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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241 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/deepsea.png
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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242 :width: 400
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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243 :alt: deapsea model configuration
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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244 ]]>
6ff2f197bc35 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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245 </help>
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246 <expand macro="sklearn_citation">
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247 <citation type="bibtex">
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248 @online{plotly,
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249 author = {Plotly Technologies Inc.},
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250 title = {Collaborative data science},
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251 publisher = {Plotly Technologies Inc.},
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252 address = {Montreal, QC},
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253 year = {2015},
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254 url = {https://plot.ly}}
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255 </citation>
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256 </expand>
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257 </tool>