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comparison ml_visualization_ex.xml @ 4:1b2f7d4ee4e7 draft

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"planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
author bgruening
date Mon, 16 Dec 2019 10:01:02 +0000
parents 64126fb634b5
children 1ab959d4a5ee
comparison
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3:b2d539c75654 4:1b2f7d4ee4e7
2 <description>includes several types of plotting for machine learning</description> 2 <description>includes several types of plotting for machine learning</description>
3 <macros> 3 <macros>
4 <import>main_macros.xml</import> 4 <import>main_macros.xml</import>
5 <import>keras_macros.xml</import> 5 <import>keras_macros.xml</import>
6 </macros> 6 </macros>
7 <expand macro="python_requirements"> 7 <expand macro="python_requirements"/>
8 <requirement type="package" version="3.1.1">plotly</requirement>
9 <requirement type="package" version="2.40.1">graphviz</requirement>
10 <requirement type="package" version="1.4.1">pydot</requirement>
11 </expand>
12 <expand macro="macro_stdio"/> 8 <expand macro="macro_stdio"/>
13 <version_command>echo "@VERSION@"</version_command> 9 <version_command>echo "@VERSION@"</version_command>
14 <command> 10 <command>
15 <![CDATA[ 11 <![CDATA[
16 python '$__tool_directory__/ml_visualization_ex.py' 12 python '$__tool_directory__/ml_visualization_ex.py'
43 </param> 39 </param>
44 <when value="learning_curve"> 40 <when value="learning_curve">
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."/> 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."/>
46 <param name="plot_std_err" type="boolean" truevalue="booltrue" falsevalue="boolfalse" optional="true" checked="false" label="Whether to plot standard error bar?"/> 42 <param name="plot_std_err" type="boolean" truevalue="booltrue" falsevalue="boolfalse" optional="true" checked="false" label="Whether to plot standard error bar?"/>
47 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/> 43 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
44 <param name="plot_format" type="select" label="The output format and library">
45 <option value="html" selected="true">An interactive html by plotly</option>
46 <!--<option value="png">PNG image by matplotlib</option> TODO-->
47 </param>
48 </when> 48 </when>
49 <when value="pr_curve"> 49 <when value="pr_curve">
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."/> 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."/>
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."/> 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."/>
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."/> 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."/>
53 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/> 53 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
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."/>
55 <param name="plot_format" type="select" label="The output format and library">
56 <option value="plotly_html" selected="true">An interactive html by plotly</option>
57 <option value="matplotlib_svg">SVG image by matplotlib</option>
58 </param>
54 </when> 59 </when>
55 <when value="roc_curve"> 60 <when value="roc_curve">
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."/> 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."/>
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."/> 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."/>
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."/> 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."/>
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."/> 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."/>
60 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/> 65 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
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."/>
67 <param name="plot_format" type="select" label="The output format and library">
68 <option value="plotly_html" selected="true">An interactive html by plotly</option>
69 <option value="matplotlib_svg">SVG image by matplotlib</option>
70 </param>
61 </when> 71 </when>
62 <when value="rfecv_gridscores"> 72 <when value="rfecv_gridscores">
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_`."/> 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_`."/>
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]`."/> 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]`."/>
65 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/> 75 <param name="title" type="text" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
76 <param name="plot_format" type="select" label="The output format and library">
77 <option value="html" selected="true">An interactive html by plotly</option>
78 <!--<option value="png">PNG image by matplotlib</option> TODO-->
79 </param>
66 </when> 80 </when>
67 <when value="feature_importances"> 81 <when value="feature_importances">
68 <param name="infile_estimator" type="data" format="zip" label="Select the dataset containing fitted estimator/pipeline" /> 82 <param name="infile_estimator" type="data" format="zip" label="Select the dataset containing fitted estimator/pipeline" />
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."/> 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."/>
70 <conditional name="column_selector_options"> 84 <conditional name="column_selector_options">
71 <expand macro="samples_column_selector_options" multiple="true"/> 85 <expand macro="samples_column_selector_options" multiple="true"/>
72 </conditional> 86 </conditional>
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."/> 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."/>
74 <param name="title" type="text" value="" optional="true" label="Custom plot title" help="Optional."/> 88 <param name="title" type="text" value="" optional="true" label="Custom plot title" help="Optional."/>
89 <param name="plot_format" type="select" label="The output format and library">
90 <option value="html" selected="true">An interactive html by plotly</option>
91 <!--<option value="png">PNG image by matplotlib</option> TODO-->
92 </param>
75 </when> 93 </when>
76 <when value="keras_plot_model"> 94 <when value="keras_plot_model">
77 <param name="infile_model_config" type="data" format="json" label="Select the JSON dataset containing configuration for a neural network model"/> 95 <param name="infile_model_config" type="data" format="json" label="Select the JSON dataset containing configuration for a neural network model"/>
78 <param name="title" type="hidden" value="" optional="true" label="Plot title" help="Optional. If change is desired."/> 96 <param name="title" type="hidden" value="" optional="true" label="Plot title" help="Optional. If change is desired."/>
97 <param name="plot_format" type="hidden" value="png" label="The output format and library"/>
79 </when> 98 </when>
80 </conditional> 99 </conditional>
81 </inputs> 100 </inputs>
82 <outputs> 101 <outputs>
83 <data name="output" format="html" from_work_dir="output" label="${plotting_selection.plot_type} plot on ${on_string}"> 102 <data name="output" format="html" from_work_dir="output" label="${plotting_selection.plot_type} plot on ${on_string}">
84 <change_format> 103 <change_format>
85 <when input="plotting_selection.plot_type" value="keras_plot_model" format="png"/> 104 <when input="plotting_selection.plot_format" value="png" format="png"/>
86 </change_format> 105 </change_format>
87 </data> 106 </data>
88 </outputs> 107 </outputs>
89 <tests> 108 <tests>
90 <test> 109 <test>