Mercurial > repos > bgruening > plotly_regression_performance_plots

annotate plot_regression_performance.py @ 0:0800a1b66bbd draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
author bgruening
date Thu, 08 Nov 2018 13:28:04 -0500
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children 389227fa1864
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0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
bgruening
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diff changeset
1 import argparse
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
bgruening
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2 import pandas as pd
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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3 import plotly
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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4 import plotly.graph_objs as go
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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7 def main(infile_input, infile_output):
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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8 """
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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9 Produce an interactive actual vs predicted curves and residual plots
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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10 Args:
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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11 infile_input: str, input tabular file with true values
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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12 infile_output: str, input tabular file with predicted values
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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13 """
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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15 df_input = pd.read_csv(infile_input, sep='\t', parse_dates=True)
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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16 df_output = pd.read_csv(infile_output, sep='\t', parse_dates=True)
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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17 true_values = df_input.iloc[:, -1].copy()
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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18 predicted_values = df_output.iloc[:, -1].copy()
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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19 axis_labels = list(range(1, len(true_values)+1))
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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21 # true vs predicted curves
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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22 trace_true = go.Scatter(
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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23 x=axis_labels,
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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24 y=true_values,
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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25 mode='lines+markers',
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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26 name='True values'
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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27 )
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29 trace_predicted = go.Scatter(
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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30 x=axis_labels,
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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31 y=predicted_values,
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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32 mode='lines+markers',
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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33 name='Predicted values'
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34 )
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36 layout_tp = go.Layout(
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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37 title='True vs predicted values',
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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38 xaxis=dict(title='Number of data points'),
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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39 yaxis=dict(title='Values')
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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40 )
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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42 data_tp = [trace_true, trace_predicted]
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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43 fig_tp = go.Figure(data=data_tp, layout=layout_tp)
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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44 plotly.offline.plot(fig_tp, filename="output_actual_vs_pred.html", auto_open=False)
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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45
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46 # scatter plot
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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47 max_tv = int(max(true_values))
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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48 x_y_values = list(range(0, max_tv))
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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49
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50 trace_x_eq_y = go.Scatter(
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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51 x=x_y_values,
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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52 y=x_y_values,
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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53 mode='lines',
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54 name='X = Y curve'
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55 )
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56
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57 trace_true_pred = go.Scatter(
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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58 x=true_values,
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59 y=predicted_values,
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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60 mode='markers',
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61 name='True and predicted values'
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62 )
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63
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64 layout_true_pred = go.Layout(
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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65 title='True vs predicted values',
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66 xaxis=dict(title='True values'),
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67 yaxis=dict(title='Predicted values')
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68 )
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69
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70 data_true_pred = [trace_true_pred, trace_x_eq_y]
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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71 fig_true_pred = go.Figure(data=data_true_pred, layout=layout_true_pred)
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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72 plotly.offline.plot(fig_true_pred, filename="output_scatter_plot.html", auto_open=False)
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74 # residual plot
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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75 residual = predicted_values - true_values
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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76 trace_residual = go.Scatter(
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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77 x=predicted_values,
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78 y=residual,
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79 mode='markers'
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80 )
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81
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82 layout_residual = go.Layout(
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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83 title='Residual vs predicted values',
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84 xaxis=dict(title='Predicted values'),
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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85 yaxis=dict(title='Residual (Predicted - True)')
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
bgruening
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86 )
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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87
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
bgruening
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88 data_residual = [trace_residual]
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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89 fig_residual = go.Figure(data=data_residual, layout=layout_residual)
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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90 plotly.offline.plot(fig_residual, filename="output_residual_plot.html", auto_open=False)
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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91
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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92
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
bgruening
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93 if __name__ == "__main__":
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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94 aparser = argparse.ArgumentParser()
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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95 aparser.add_argument("-i", "--input", dest="infile_input", required=True)
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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96 aparser.add_argument("-j", "--output", dest="infile_output", required=True)
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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97 args = aparser.parse_args()
0800a1b66bbd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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98 main(args.infile_input, args.infile_output)