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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit 2473a53fde6d8e646e90d2a5201999c8c6a48695
author bgruening
date Wed, 09 Jan 2019 02:56:53 -0500
parents 157659f94256
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157659f94256 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
157659f94256 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
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ca5ffd01f136 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit 2473a53fde6d8e646e90d2a5201999c8c6a48695
bgruening
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3 import numpy as np
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157659f94256 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
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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5 import plotly.graph_objs as go
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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8 def main(infile_input, infile_output):
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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9 """
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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10 Produce an interactive actual vs predicted curves and residual plots
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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11 Args:
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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12 infile_input: str, input tabular file with true values
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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13 infile_output: str, input tabular file with predicted values
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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14 """
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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16 df_input = pd.read_csv(infile_input, sep='\t', parse_dates=True)
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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17 df_output = pd.read_csv(infile_output, sep='\t', parse_dates=True)
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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18 true_values = df_input.iloc[:, -1].copy()
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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19 predicted_values = df_output.iloc[:, -1].copy()
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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20 axis_labels = list(range(1, len(true_values)+1))
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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22 # true vs predicted curves
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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23 trace_true = go.Scatter(
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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24 x=axis_labels,
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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25 y=true_values,
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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26 mode='lines+markers',
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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27 name='True values'
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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28 )
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30 trace_predicted = go.Scatter(
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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31 x=axis_labels,
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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32 y=predicted_values,
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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33 mode='lines+markers',
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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34 name='Predicted values'
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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35 )
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37 layout_tp = go.Layout(
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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38 title='True vs predicted values',
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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39 xaxis=dict(title='Number of data points'),
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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40 yaxis=dict(title='Values')
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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41 )
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43 data_tp = [trace_true, trace_predicted]
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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44 fig_tp = go.Figure(data=data_tp, layout=layout_tp)
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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45 plotly.offline.plot(fig_tp, filename="output_actual_vs_pred.html", auto_open=False)
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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47 # scatter plot
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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48 max_tv = int(max(true_values))
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49 x_y_values = list(range(0, max_tv))
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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50
1
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51 true_mean = np.mean(true_values)
ca5ffd01f136 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit 2473a53fde6d8e646e90d2a5201999c8c6a48695
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52 res_true_predicted = np.sum((true_values - predicted_values) ** 2)
ca5ffd01f136 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit 2473a53fde6d8e646e90d2a5201999c8c6a48695
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53 res_total = np.sum((true_values - true_mean) ** 2)
ca5ffd01f136 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit 2473a53fde6d8e646e90d2a5201999c8c6a48695
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54 r2 = 1 - (res_true_predicted / float(res_total))
ca5ffd01f136 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit 2473a53fde6d8e646e90d2a5201999c8c6a48695
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55 rmse = np.sqrt(np.mean([(x - y) ** 2 for x, y in zip(true_values, predicted_values)]))
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56
0
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57 trace_x_eq_y = go.Scatter(
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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58 x=x_y_values,
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59 y=x_y_values,
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60 mode='lines',
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61 name='X = Y curve'
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62 )
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64 trace_true_pred = go.Scatter(
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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65 x=true_values,
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66 y=predicted_values,
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67 mode='markers',
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68 name='True and predicted values'
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69 )
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71 layout_true_pred = go.Layout(
1
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72 title='True vs predicted values (RMSE: %s, R2: %s)' % (str(np.round(rmse, 2)), str(np.round(r2, 2))),
0
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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73 xaxis=dict(title='True values'),
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74 yaxis=dict(title='Predicted values')
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75 )
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77 data_true_pred = [trace_true_pred, trace_x_eq_y]
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78 fig_true_pred = go.Figure(data=data_true_pred, layout=layout_true_pred)
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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79 plotly.offline.plot(fig_true_pred, filename="output_scatter_plot.html", auto_open=False)
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81 # residual plot
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82 residual = predicted_values - true_values
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83 trace_residual = go.Scatter(
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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84 x=predicted_values,
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85 y=residual,
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86 mode='markers'
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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87 )
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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88
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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89 layout_residual = go.Layout(
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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90 title='Residual vs predicted values',
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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91 xaxis=dict(title='Predicted values'),
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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92 yaxis=dict(title='Residual (Predicted - True)')
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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93 )
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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94
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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95 data_residual = [trace_residual]
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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96 fig_residual = go.Figure(data=data_residual, layout=layout_residual)
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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97 plotly.offline.plot(fig_residual, filename="output_residual_plot.html", auto_open=False)
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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98
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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99
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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100 if __name__ == "__main__":
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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101 aparser = argparse.ArgumentParser()
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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102 aparser.add_argument("-i", "--input", dest="infile_input", required=True)
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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103 aparser.add_argument("-j", "--output", dest="infile_output", required=True)
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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104 args = aparser.parse_args()
157659f94256 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/plotly_regression_performance_plots commit c17efec384ad7438f54675fae1ab0c3a57c22869
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105 main(args.infile_input, args.infile_output)