Mercurial > repos > bgruening > ml_visualization_ex

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
author bgruening
date Wed, 02 Oct 2019 03:50:11 -0400
parents f96efab83b65
children 6b94d76a1397
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1 <tool id="ml_visualization_ex" name="Machine Learning Visualization Extension" version="@VERSION@">
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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 <requirement type="package" version="3.1.1">plotly</requirement>
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9 <requirement type="package" version="2.40.1">graphviz</requirement>
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10 <requirement type="package" version="1.4.1">pydot</requirement>
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11 </expand>
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12 <expand macro="macro_stdio"/>
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13 <version_command>echo "@VERSION@"</version_command>
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14 <command>
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15 <![CDATA[
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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16 python '$__tool_directory__/ml_visualization_ex.py'
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17 --inputs '$inputs'
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18 #if $plotting_selection.plot_type in ['learning_curve', 'rfecv_gridscores']
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19 --infile1 '$plotting_selection.infile1'
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20 #elif $plotting_selection.plot_type in ['pr_curve', 'roc_curve']
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21 --infile1 '$plotting_selection.infile1'
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22 --infile2 '$plotting_selection.infile2'
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23 #elif $plotting_selection.plot_type == 'feature_importances'
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24 --estimator '$plotting_selection.infile_estimator'
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25 --infile1 '$plotting_selection.infile1'
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26 #elif $plotting_selection.plot_type == 'keras_plot_model'
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27 --model_config '$plotting_selection.infile_model_config'
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28 #end if
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29 ]]>
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30 </command>
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31 <configfiles>
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32 <inputs name="inputs" />
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33 </configfiles>
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34 <inputs>
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35 <conditional name="plotting_selection">
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36 <param name="plot_type" type="select" label="Select a plotting type">
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37 <option value="learning_curve" selected="true">Learning curve</option>
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38 <option value="pr_curve">2-class / multpi-label Precison Recall curve</option>
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39 <option value="roc_curve">2-class / multi-label Receiver Operating Characteristic (ROC) curve</option>
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40 <option value="rfecv_gridscores">Number of features vs. Recursive Feature Elimination gridscores with corss-validation</option>
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41 <option value="feature_importances">Feature Importances plot</option>
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42 <option value="keras_plot_model">keras plot model - plot configuration of a neural network model</option>
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43 </param>
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44 <when value="learning_curve">
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45 <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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46 <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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47 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
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48 </when>
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49 <when value="pr_curve">
1
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50 <param name="infile1" type="data" format="tabular" label="Select the dataset containing true labels." help="No headers. 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="No headers. For 2-class, sinle column or the first column contains scores for the positive label. For multi-label, each column corresponds to one label."/>
0
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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 </when>
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55 <when value="roc_curve">
1
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56 <param name="infile1" type="data" format="tabular" label="Select the dataset containing true labels." help="No headers. 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="No headers. For 2-class, sinle column or the first column contains scores for the positive label. For multi-label, each column corresponds to one label."/>
0
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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="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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60 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
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61 </when>
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62 <when value="rfecv_gridscores">
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63 <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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64 <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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65 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
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66 </when>
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67 <when value="feature_importances">
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68 <param name="infile_estimator" type="data" format="zip" label="Select the dataset containing fitted estimator/pipeline" />
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69 <param name="infile1" type="data" format="tabular" label="Select the dataset containing feature names" help="Make sure the headers (first row) are feature names."/>
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70 <conditional name="column_selector_options">
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71 <expand macro="samples_column_selector_options" multiple="true"/>
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72 </conditional>
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73 <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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74 <param name="title" type="text" value="" optional="true" label="Custom plot title" help="Optional."/>
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75 </when>
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76 <when value="keras_plot_model">
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77 <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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78 <param name="title" type="hidden" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
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79 </when>
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80 </conditional>
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81 </inputs>
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82 <outputs>
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83 <data name="output" format="html" from_work_dir="output" label="${plotting_selection.plot_type} plot on ${on_string}">
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84 <change_format>
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85 <when input="plotting_selection.plot_type" value="keras_plot_model" format="png"/>
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86 </change_format>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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87 </data>
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88 </outputs>
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89 <tests>
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90 <test>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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91 <param name="plot_type" value="roc_curve"/>
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92 <param name="infile1" value="y_true.tabular" ftype="tabular"/>
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93 <param name="infile2" value="y_score.tabular" ftype="tabular"/>
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94 <output name="output" file="ml_vis04.html" compare="sim_size"/>
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95 </test>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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96 <test>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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97 <param name="plot_type" value="feature_importances"/>
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98 <param name="infile_estimator" value="best_estimator_.zip" ftype="zip"/>
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99 <param name="infile1" value="regression_X.tabular" ftype="tabular"/>
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100 <param name="selected_column_selector_option" value="all_columns"/>
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101 <output name="output" file="ml_vis01.html" compare="sim_size"/>
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102 </test>
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103 <test>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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104 <param name="plot_type" value="learning_curve"/>
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105 <param name="infile1" value="mv_result03.tabular" ftype="tabular"/>
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106 <output name="output" file="ml_vis02.html" compare="sim_size"/>
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107 </test>
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108 <test>
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109 <param name="plot_type" value="pr_curve"/>
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110 <param name="infile1" value="y_true.tabular" ftype="tabular"/>
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111 <param name="infile2" value="y_score.tabular" ftype="tabular"/>
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112 <output name="output" file="ml_vis03.html" compare="sim_size"/>
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113 </test>
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114 <test>
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115 <param name="plot_type" value="rfecv_gridscores"/>
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116 <param name="infile1" value="grid_scores_.tabular" ftype="tabular"/>
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117 <output name="output" file="ml_vis05.html" compare="sim_size"/>
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118 </test>
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119 <test>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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120 <param name="plot_type" value="keras_plot_model"/>
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121 <param name="infile_model_config" value="deepsear_1feature.json" ftype="json"/>
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122 <output name="output" file="ml_vis05.png" compare="sim_size" delta="20000"/>
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123 </test>
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124 </tests>
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125 <help>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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126 <![CDATA[
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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127 **What it does**
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128 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.
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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129
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130
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131 **Feature importances**
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132
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133 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/feature_importances.png
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134 :width: 400
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135 :alt: feature importances
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136
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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137
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138 **Learning curve**
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139
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140 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/learning_curve.png
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141 :width: 400
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142 :alt: learning curve
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143
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144
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145 **Precison recall curve**
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146
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147 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/pr_curve.png
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148 :width: 400
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149 :alt: precison recall curve
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150
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151
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152 **Receiver operating characteristic curve**
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153
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154 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/roc_curve.png
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155 :width: 400
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156 :alt: Receiver operating characteristic curve
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157
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158
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159 **Number of featues vs. rfecv gridscores**
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160
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161 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/rfecv_gridscore.png
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162 :width: 400
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163 :alt: Number of featues vs. rfecv gridscores
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164
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165
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166 **Deep learning model configuration**
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167
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168 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/deepsea.png
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169 :width: 400
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170 :alt: deapsea model configuration
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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171 ]]>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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172 </help>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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173 <expand macro="sklearn_citation">
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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174 <citation type="bibtex">
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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175 @online{plotly,
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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176 author = {Plotly Technologies Inc.},
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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177 title = {Collaborative data science},
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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178 publisher = {Plotly Technologies Inc.},
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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179 address = {Montreal, QC},
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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180 year = {2015},
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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181 url = {https://plot.ly}}
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182 </citation>
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183 </expand>
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184 </tool>