Mercurial > repos > bgruening > ml_visualization_ex

annotate ml_visualization_ex.xml @ 14:9c19cf3c4ea0 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 13:08:43 +0000
parents 6cf6f27547cb
children a536d2736c2d
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14
9c19cf3c4ea0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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1 <tool id="ml_visualization_ex" name="Machine Learning Visualization Extension" version="@VERSION@" profile="@PROFILE@">
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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>
8
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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 #end if
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25 ]]>
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26 </command>
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27 <configfiles>
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28 <inputs name="inputs" />
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29 </configfiles>
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30 <inputs>
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31 <conditional name="plotting_selection">
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32 <param name="plot_type" type="select" label="Select a plotting type">
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33 <option value="learning_curve" selected="true">Learning curve</option>
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34 <option value="pr_curve">2-class / multpi-label Precison Recall curve</option>
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35 <option value="roc_curve">2-class / multi-label Receiver Operating Characteristic (ROC) curve</option>
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36 <option value="rfecv_gridscores">Number of features vs. Recursive Feature Elimination gridscores with corss-validation</option>
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37 <option value="feature_importances">Feature Importances plot</option>
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38 <option value="keras_plot_model">keras plot model - plot configuration of a neural network model</option>
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39 </param>
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40 <when value="learning_curve">
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41 <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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42 <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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43 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
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44 <param name="plot_format" type="select" label="The output format and library">
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45 <option value="html" selected="true">An interactive html by plotly</option>
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46 <!--<option value="png">PNG image by matplotlib</option> TODO-->
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47 </param>
0
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48 </when>
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49 <when value="pr_curve">
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50 <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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51 <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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52 <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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53 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
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54 <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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55 <param name="plot_format" type="select" label="The output format and library">
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56 <option value="plotly_html" selected="true">An interactive html by plotly</option>
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57 <option value="matplotlib_svg">SVG image by matplotlib</option>
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58 </param>
0
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59 </when>
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60 <when value="roc_curve">
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61 <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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62 <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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63 <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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64 <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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65 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
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66 <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." />
4
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67 <param name="plot_format" type="select" label="The output format and library">
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68 <option value="plotly_html" selected="true">An interactive html by plotly</option>
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69 <option value="matplotlib_svg">SVG image by matplotlib</option>
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70 </param>
0
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71 </when>
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72 <when value="rfecv_gridscores">
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73 <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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74 <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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75 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
4
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76 <param name="plot_format" type="select" label="The output format and library">
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77 <option value="html" selected="true">An interactive html by plotly</option>
6b94d76a1397 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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78 <!--<option value="png">PNG image by matplotlib</option> TODO-->
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79 </param>
0
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80 </when>
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81 <when value="feature_importances">
14
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82 <param name="infile_estimator" type="data" format="h5mlm" label="Select the dataset containing fitted estimator/pipeline" />
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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83 <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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84 <conditional name="column_selector_options">
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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85 <expand macro="samples_column_selector_options" multiple="true" />
0
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86 </conditional>
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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87 <param name="threshold" type="float" value="" optional="true" min="0." label="Threshold value" help="Features with importance below the threshold value will be ignored." />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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88 <param name="title" type="text" value="" optional="true" label="Custom plot title" help="Optional." />
4
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89 <param name="plot_format" type="select" label="The output format and library">
6b94d76a1397 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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90 <option value="html" selected="true">An interactive html by plotly</option>
6b94d76a1397 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
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91 <!--<option value="png">PNG image by matplotlib</option> TODO-->
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92 </param>
0
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93 </when>
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94 <when value="keras_plot_model">
8
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95 <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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96 <param name="title" type="hidden" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
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97 <param name="plot_format" type="hidden" value="png" label="The output format and library" />
0
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98 </when>
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99 </conditional>
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100 </inputs>
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101 <outputs>
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102 <data name="output" format="html" from_work_dir="output" label="${plotting_selection.plot_type} plot on ${on_string}">
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103 <change_format>
8
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104 <when input="plotting_selection.plot_format" value="png" format="png" />
0
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105 </change_format>
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106 </data>
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107 </outputs>
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108 <tests>
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109 <test>
8
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110 <param name="plot_type" value="roc_curve" />
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111 <param name="infile1" value="y_true.tabular" ftype="tabular" />
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112 <param name="infile2" value="y_score.tabular" ftype="tabular" />
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113 <output name="output" file="ml_vis04.html" compare="sim_size" />
0
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114 </test>
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115 <test>
8
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116 <param name="plot_type" value="feature_importances" />
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117 <param name="infile_estimator" value="best_estimator_.h5mlm" ftype="h5mlm" />
8
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118 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
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119 <param name="selected_column_selector_option" value="all_columns" />
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120 <output name="output" file="ml_vis01.html" compare="sim_size" />
0
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121 </test>
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122 <test>
8
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123 <param name="plot_type" value="learning_curve" />
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124 <param name="infile1" value="mv_result03.tabular" ftype="tabular" />
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125 <output name="output" file="ml_vis02.html" compare="sim_size" />
0
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126 </test>
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127 <test>
8
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128 <param name="plot_type" value="pr_curve" />
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129 <param name="infile1" value="y_true.tabular" ftype="tabular" />
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130 <param name="infile2" value="y_score.tabular" ftype="tabular" />
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131 <output name="output" file="ml_vis03.html" compare="sim_size" />
0
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132 </test>
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133 <test>
8
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134 <param name="plot_type" value="rfecv_gridscores" />
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135 <param name="infile1" value="grid_scores_.tabular" ftype="tabular" />
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136 <output name="output" file="ml_vis05.html" compare="sim_size" />
0
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137 </test>
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138 <test>
8
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139 <param name="plot_type" value="keras_plot_model" />
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140 <param name="infile_model_config" value="deepsear_1feature.json" ftype="json" />
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141 <output name="output" file="ml_vis05.png" compare="sim_size" delta="20000" />
0
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142 </test>
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143 </tests>
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144 <help>
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145 <![CDATA[
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146 **What it does**
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147 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.
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148
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149
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150 **Feature importances**
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151
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152 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/feature_importances.png
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153 :width: 400
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154 :alt: feature importances
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155
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156
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157 **Learning curve**
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158
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159 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/learning_curve.png
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160 :width: 400
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161 :alt: learning curve
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162
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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163
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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164 **Precison recall curve**
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165
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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166 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/pr_curve.png
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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167 :width: 400
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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168 :alt: precison recall curve
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169
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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170
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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171 **Receiver operating characteristic curve**
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172
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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173 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/roc_curve.png
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174 :width: 400
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175 :alt: Receiver operating characteristic curve
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176
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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177
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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178 **Number of featues vs. rfecv gridscores**
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179
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180 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/rfecv_gridscore.png
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181 :width: 400
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182 :alt: Number of featues vs. rfecv gridscores
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183
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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184
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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185 **Deep learning model configuration**
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186
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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187 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/deepsea.png
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188 :width: 400
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189 :alt: deapsea model configuration
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190 ]]>
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191 </help>
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192 <expand macro="sklearn_citation">
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193 <citation type="bibtex">
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194 @online{plotly,
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195 author = {Plotly Technologies Inc.},
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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196 title = {Collaborative data science},
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197 publisher = {Plotly Technologies Inc.},
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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198 address = {Montreal, QC},
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199 year = {2015},
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200 url = {https://plot.ly}}
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201 </citation>
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202 </expand>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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203 </tool>