Mercurial > repos > bgruening > ml_visualization_ex

annotate ml_visualization_ex.xml @ 16:a536d2736c2d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
author bgruening
date Fri, 22 Sep 2023 16:40:38 +0000
parents 9c19cf3c4ea0
children
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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>
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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>
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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">
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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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_`." />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 6
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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]`." />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 6
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81 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
4
6b94d76a1397 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 1
diff changeset
82 <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"
bgruening
parents: 1
diff changeset
83 <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"
bgruening
parents: 1
diff changeset
84 <!--<option value="png">PNG image by matplotlib</option> TODO-->
6b94d76a1397 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 1
diff changeset
85 </param>
0
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
86 </when>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
bgruening
parents:
diff changeset
87 <when value="feature_importances">
14
9c19cf3c4ea0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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diff changeset
88 <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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diff changeset
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
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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diff changeset
90 <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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parents: 6
diff changeset
91 <expand macro="samples_column_selector_options" multiple="true" />
0
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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diff changeset
92 </conditional>
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
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." />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 6
diff changeset
94 <param name="title" type="text" value="" optional="true" label="Custom plot title" help="Optional." />
4
6b94d76a1397 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 1
diff changeset
95 <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"
bgruening
parents: 1
diff changeset
96 <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"
bgruening
parents: 1
diff changeset
97 <!--<option value="png">PNG image by matplotlib</option> TODO-->
6b94d76a1397 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 1
diff changeset
98 </param>
0
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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diff changeset
99 </when>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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100 <when value="keras_plot_model">
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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diff changeset
101 <param name="infile_model_config" type="data" format="json" label="Select the JSON dataset containing configuration for a neural network model" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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102 <param name="title" type="hidden" value="" optional="true" label="Plot title" help="Optional. If change is desired." />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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parents: 6
diff changeset
103 <param name="plot_format" type="hidden" value="png" label="The output format and library" />
0
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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104 </when>
16
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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105 <when value="classification_confusion_matrix">
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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106 <param name="infile_true" type="data" format="tabular" label="Select dataset containing true labels" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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107 <param name="header_true" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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108 <conditional name="column_selector_options_true">
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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109 <expand macro="samples_column_selector_options" multiple="true" column_option="selected_column_selector_option" col_name="col1" infile="infile_true" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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110 </conditional>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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111
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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112 <param name="infile_predicted" type="data" format="tabular" label="Select dataset containing predicted labels" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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113 <param name="header_predicted" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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114 <param name="title" type="text" value="Confusion matrix between true and predicted labels" label="Plot title" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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115 <param name="plot_format" type="hidden" value="png" label="The output format and library" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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116 <param name="plot_color" type="select" label="Choose plot color">
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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117 <option value="Greys">Greys</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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118 <option value="Purples">Purples</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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119 <option value="Blues">Blues</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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120 <option value="Greens" selected="true">Greens</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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121 <option value="Oranges">Oranges</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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122 <option value="Reds">Reds</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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123 <option value="Summer">Summer</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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124 <option value="Autumn">Autumn</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
bgruening
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125 <option value="RdYlGn">RdYlGn</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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126 <option value="Spectral">Spectral</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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127 <option value="winter">winter</option>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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128 </param>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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129 </when>
0
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130 </conditional>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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131 </inputs>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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132 <outputs>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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133 <data name="output" format="html" from_work_dir="output" label="${plotting_selection.plot_type} plot on ${on_string}">
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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134 <change_format>
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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135 <when input="plotting_selection.plot_format" value="png" format="png" />
0
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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136 </change_format>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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137 </data>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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138 </outputs>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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139 <tests>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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140 <test>
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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141 <param name="plot_type" value="roc_curve" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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142 <param name="infile1" value="y_true.tabular" ftype="tabular" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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143 <param name="infile2" value="y_score.tabular" ftype="tabular" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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144 <output name="output" file="ml_vis04.html" compare="sim_size" />
0
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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145 </test>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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146 <test>
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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147 <param name="plot_type" value="feature_importances" />
14
9c19cf3c4ea0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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148 <param name="infile_estimator" value="best_estimator_.h5mlm" ftype="h5mlm" />
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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149 <param name="infile1" value="regression_X.tabular" ftype="tabular" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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150 <param name="selected_column_selector_option" value="all_columns" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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151 <output name="output" file="ml_vis01.html" compare="sim_size" />
0
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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152 </test>
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153 <test>
8
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154 <param name="plot_type" value="learning_curve" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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155 <param name="infile1" value="mv_result03.tabular" ftype="tabular" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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156 <output name="output" file="ml_vis02.html" compare="sim_size" />
0
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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157 </test>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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158 <test>
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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159 <param name="plot_type" value="pr_curve" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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160 <param name="infile1" value="y_true.tabular" ftype="tabular" />
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161 <param name="infile2" value="y_score.tabular" ftype="tabular" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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162 <output name="output" file="ml_vis03.html" compare="sim_size" />
0
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163 </test>
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164 <test>
8
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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165 <param name="plot_type" value="rfecv_gridscores" />
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166 <param name="infile1" value="grid_scores_.tabular" ftype="tabular" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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167 <output name="output" file="ml_vis05.html" compare="sim_size" />
0
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168 </test>
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169 <test>
8
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170 <param name="plot_type" value="keras_plot_model" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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171 <param name="infile_model_config" value="deepsear_1feature.json" ftype="json" />
6cf6f27547cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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172 <output name="output" file="ml_vis05.png" compare="sim_size" delta="20000" />
0
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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173 </test>
16
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174 <test>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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175 <param name="plot_type" value="classification_confusion_matrix" />
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176 <param name="infile_true" value="ml_confusion_true.tabular" ftype="tabular" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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177 <param name="header_true" value="False" />
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178 <param name="selected_column_selector_option" value="all_columns" />
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179 <param name="infile_predicted" value="ml_confusion_predicted.tabular" ftype="tabular" />
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180 <param name="header_predicted" value="False" />
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181 <param name="title" value="Confusion matrix" />
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182 <param name="plot_color" value="winter" />
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183 <output name="output" file="ml_confusion_viz.png" compare="sim_size" />
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184 </test>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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185 <test>
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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186 <param name="plot_type" value="classification_confusion_matrix" />
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187 <param name="infile_true" value="true_header.tabular" ftype="tabular" />
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188 <param name="header_true" value="True" />
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189 <param name="selected_column_selector_option" value="all_columns" />
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190 <param name="infile_predicted" value="predicted_header.tabular" ftype="tabular" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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191 <param name="header_predicted" value="True" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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192 <param name="title" value="Confusion matrix" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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193 <param name="plot_color" value="winter" />
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194 <output name="output" file="ml_confusion_viz.png" compare="sim_size" />
a536d2736c2d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 3c1e6c72303cfd8a5fd014734f18402b97f8ecb5
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195 </test>
0
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196 </tests>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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197 <help>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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198 <![CDATA[
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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199 **What it does**
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200 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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201
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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202
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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203 **Feature importances**
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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204
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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205 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/feature_importances.png
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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206 :width: 400
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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207 :alt: feature importances
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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208
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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209
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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210 **Learning curve**
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211
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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212 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/learning_curve.png
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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213 :width: 400
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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214 :alt: learning curve
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215
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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216
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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217 **Precison recall curve**
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218
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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219 .. 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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220 :width: 400
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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221 :alt: precison recall curve
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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222
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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223
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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224 **Receiver operating characteristic curve**
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225
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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226 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/roc_curve.png
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227 :width: 400
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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228 :alt: Receiver operating characteristic curve
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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229
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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230
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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231 **Number of featues vs. rfecv gridscores**
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232
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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233 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/rfecv_gridscore.png
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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234 :width: 400
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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235 :alt: Number of featues vs. rfecv gridscores
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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236
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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237
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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238 **Deep learning model configuration**
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239
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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240 .. image:: https://raw.githubusercontent.com/goeckslab/Galaxy-ML/master/galaxy_ml/tools/images/deepsea.png
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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241 :width: 400
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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242 :alt: deapsea model configuration
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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243 ]]>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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244 </help>
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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245 <expand macro="sklearn_citation">
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246 <citation type="bibtex">
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247 @online{plotly,
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248 author = {Plotly Technologies Inc.},
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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249 title = {Collaborative data science},
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250 publisher = {Plotly Technologies Inc.},
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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251 address = {Montreal, QC},
f96efab83b65 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit ba6a47bdf76bbf4cb276206ac1a8cbf61332fd16"
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252 year = {2015},
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253 url = {https://plot.ly}}
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254 </citation>
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255 </expand>
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256 </tool>