Mercurial > repos > bgruening > sklearn_generalized_linear
annotate generalized_linear.xml @ 8:0203a713874e draft
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
author | bgruening |
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date | Tue, 22 May 2018 19:33:01 -0400 |
parents | fd6c50f21cd0 |
children | 44699d79d908 |
rev | line source |
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0
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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1 <tool id="sklearn_generalized_linear" name="Generalized linear models" version="@VERSION@"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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2 <description>for classification and regression</description> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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3 <macros> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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4 <import>main_macros.xml</import> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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5 </macros> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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6 <expand macro="python_requirements"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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7 <expand macro="macro_stdio"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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8 <version_command>echo "@VERSION@"</version_command> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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9 <command><![CDATA[ |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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10 python "$glm_script" '$inputs' |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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11 ]]> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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12 </command> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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13 <configfiles> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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14 <inputs name="inputs"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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15 <configfile name="glm_script"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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16 <![CDATA[ |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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17 import sys |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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18 import json |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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19 import numpy as np |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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20 import sklearn.linear_model |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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21 import pandas |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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22 import pickle |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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23 from scipy.io import mmread |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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24 |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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25 @COLUMNS_FUNCTION@ |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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26 |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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27 input_json_path = sys.argv[1] |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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28 params = json.load(open(input_json_path, "r")) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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29 |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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30 #if $selected_tasks.selected_task == "train": |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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31 |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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32 algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"] |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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33 options = params["selected_tasks"]["selected_algorithms"]["options"] |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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34 |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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35 #if $selected_tasks.selected_algorithms.input_options.selected_input=="tabular": |
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fd6c50f21cd0
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466
bgruening
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36 header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header1"] else None |
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3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
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37 X = read_columns( |
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
bgruening
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38 "$selected_tasks.selected_algorithms.input_options.infile1", |
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
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39 "$selected_tasks.selected_algorithms.input_options.col1", |
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
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40 sep='\t', |
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fd6c50f21cd0
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466
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41 header=header, |
2
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
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42 parse_dates=True |
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
bgruening
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43 ) |
0
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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44 #else: |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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45 X = mmread(open("$selected_tasks.selected_algorithms.input_options.infile1", 'r')) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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46 #end if |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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47 |
4
fd6c50f21cd0
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466
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48 header = 'infer' if params["selected_tasks"]["selected_algorithms"]["input_options"]["header2"] else None |
2
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
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49 y = read_columns( |
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
bgruening
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50 "$selected_tasks.selected_algorithms.input_options.infile2", |
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
bgruening
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51 "$selected_tasks.selected_algorithms.input_options.col2", |
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
bgruening
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52 sep='\t', |
4
fd6c50f21cd0
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466
bgruening
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53 header=header, |
2
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
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54 parse_dates=True |
3326dd4f1e8d
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 641ac64ded23fbb6fe85d5f13926da12dcce4e76
bgruening
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55 ) |
0
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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56 |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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57 my_class = getattr(sklearn.linear_model, algorithm) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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58 estimator = my_class(**options) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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59 estimator.fit(X,y) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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60 pickle.dump(estimator,open("$outfile_fit", 'w+'), pickle.HIGHEST_PROTOCOL) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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61 |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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62 #else: |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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63 classifier_object = pickle.load(open("$selected_tasks.infile_model", 'r')) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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64 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=None, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False ) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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65 prediction = classifier_object.predict(data) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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66 prediction_df = pandas.DataFrame(prediction) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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67 res = pandas.concat([data, prediction_df], axis=1) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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68 res.to_csv(path_or_buf = "$outfile_predict", sep="\t", index=False, header=None) |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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69 #end if |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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70 |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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71 ]]> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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72 </configfile> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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73 </configfiles> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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74 <inputs> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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75 <expand macro="sl_Conditional" model="zip"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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76 <param name="selected_algorithm" type="select" label="Select a linear model:"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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77 <option value="SGDClassifier" selected="true">Stochastic Gradient Descent (SGD) classifier</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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78 <option value="SGDRegressor">Stochastic Gradient Descent (SGD) regressor</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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79 <option value="LinearRegression">Linear Regression model</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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80 <option value="RidgeClassifier">Ridge classifier</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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81 <option value="Ridge">Ridge regressor</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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82 <option value="LogisticRegression">Logistic Regression</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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83 <option value="LogisticRegressionCV">Logitic Regression with Cross Validation</option> |
32a88b3bea94
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bgruening
parents:
diff
changeset
|
84 <option value="Perceptron">Perceptron</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
85 </param> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
86 <when value="SGDClassifier"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
87 <expand macro="sl_mixed_input"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
88 <section name="options" title="Advanced Options" expanded="False"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
89 <expand macro="loss"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
90 <option value="hinge" selected="true">hinge</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
91 <option value="log">log</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
92 <option value="modified_huber">modified huber</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
93 <option value="squared_hinge">squared hinge</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
94 <option value="perceptron">perceptron</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
95 </expand> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
96 <expand macro="penalty"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
97 <expand macro="alpha"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff
changeset
|
98 <expand macro="l1_ratio"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
99 <expand macro="fit_intercept"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
|
100 <expand macro="n_iter" /> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
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101 <expand macro="shuffle"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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102 <expand macro="epsilon"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
|
103 <expand macro="learning_rate_s" selected1="true"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
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104 <expand macro="eta0"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff
changeset
|
105 <expand macro="power_t"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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106 <!--class_weight--> |
32a88b3bea94
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bgruening
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changeset
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107 <expand macro="warm_start" checked="false"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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108 <expand macro="random_state"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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109 <!--average--> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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110 </section> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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111 </when> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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112 <when value="SGDRegressor"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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113 <expand macro="sl_mixed_input"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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114 <section name="options" title="Advanced Options" expanded="False"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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115 <expand macro="loss" select="true"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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116 <expand macro="penalty"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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117 <expand macro="alpha"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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118 <expand macro="l1_ratio"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
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119 <expand macro="fit_intercept"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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120 <expand macro="n_iter" /> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
121 <expand macro="shuffle"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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|
122 <expand macro="epsilon"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
123 <expand macro="learning_rate_s" selected2="true"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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124 <expand macro="eta0" default_value="0.01"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
|
125 <expand macro="power_t" default_value="0.25"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
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126 <expand macro="warm_start" checked="false"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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|
127 <expand macro="random_state"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
128 <!--average--> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
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129 </section> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
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130 </when> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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131 <when value="LinearRegression"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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132 <expand macro="sl_mixed_input"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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|
133 <section name="options" title="Advanced Options" expanded="False"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
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134 <expand macro="fit_intercept"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
135 <expand macro="normalize"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
136 <expand macro="copy_X"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
137 </section> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
138 </when> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
|
139 <when value="RidgeClassifier"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
140 <expand macro="sl_mixed_input"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
141 <section name="options" title="Advanced Options" expanded="False"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
|
142 <expand macro="ridge_params"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
143 </section> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
144 </when> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
145 <when value="Ridge"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
146 <expand macro="sl_mixed_input"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
147 <section name="options" title="Advanced Options" expanded="False"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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148 <expand macro="ridge_params"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
149 </section> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
150 </when> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
151 <when value="LogisticRegression"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
152 <expand macro="sl_mixed_input"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
153 <section name="options" title="Advanced Options" expanded="False"> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
154 <expand macro="penalty"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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|
155 <param argument="dual" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Use dual formulation" help=" "/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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156 <expand macro="tol" default_value="0.0001" help_text="Tolerance for stopping criteria. "/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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157 <expand macro="C"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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158 <expand macro="fit_intercept"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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159 <expand macro="max_iter" default_value="100"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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|
160 <expand macro="warm_start" checked="false"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
|
161 <param argument="solver" type="select" label="Optimization algorithm" help=" "> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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|
162 <option value="liblinear" selected="true">liblinear</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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163 <option value="sag">sag</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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|
164 <option value="lbfgs">lbfgs</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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165 <option value="newton-cg">newton-cg</option> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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166 </param> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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changeset
|
167 <param argument="intercept_scaling" type="float" value="1" label="Intercept scaling factor" help="Useful only if solver is liblinear. "/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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|
168 <param argument="multi_class" type="select" label="Multiclass option" help="Works only for lbfgs solver. "> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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169 <option value="ovr" selected="true">ovr</option> |
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170 <option value="multinomial">multinomial</option> |
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171 </param> |
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172 <!--class_weight--> |
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173 <expand macro="random_state"/> |
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174 </section> |
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175 </when> |
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176 <when value="LogisticRegressionCV"> |
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177 <expand macro="sl_mixed_input"/> |
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178 <section name="options" title="Advanced Options" expanded="False"> |
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179 <param argument="Cs" type="integer" value="10" label="Inverse of regularization strength" help="A grid of Cs values are chosen in a logarithmic scale between 1e-4 and 1e4. Like in support vector machines, smaller values specify stronger regularization. "/> |
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180 <param argument="dual" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Use dual formulation" help=" "/> |
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181 <param argument="cv" type="integer" optional="true" value="" label="Number of folds used in cross validation" help="If not set, the default cross-validation generator (Stratified K-Folds) is used. "/> |
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182 <expand macro="penalty"/> |
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183 <expand macro="tol" default_value="0.0001" help_text="Tolerance for stopping criteria. "/> |
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184 <expand macro="fit_intercept"/> |
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185 <expand macro="max_iter" default_value="100"/> |
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186 <param argument="solver" type="select" label="Optimization algorithm" help=" "> |
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187 <option value="liblinear" selected="true">liblinear</option> |
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188 <option value="sag">sag</option> |
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189 <option value="lbfgs">lbfgs</option> |
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190 <option value="newton-cg">newton-cg</option> |
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191 </param> |
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192 <param argument="intercept_scaling" type="float" value="1" label="Intercept scaling factor" help="Useful only if solver is liblinear. "/> |
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193 <param argument="multi_class" type="select" label="Multiclass option" help="Works only for lbfgs solver. "> |
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194 <option value="ovr" selected="true">ovr</option> |
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195 <option value="multinomial">multinomial</option> |
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196 </param> |
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197 <param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Average scores across all folds" help=" "/> |
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198 <expand macro="random_state"/> |
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199 <!--scoring=None> |
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200 <class_weight=None--> |
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201 </section> |
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202 </when> |
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203 <when value="Perceptron"> |
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204 <expand macro="sl_mixed_input"/> |
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205 <section name="options" title="Advanced Options" expanded="False"> |
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206 <expand macro="penalty" default_value="none"/> |
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207 <expand macro="alpha"/> |
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208 <expand macro="fit_intercept"/> |
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209 <expand macro="n_iter" /> |
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210 <expand macro="shuffle"/> |
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211 <expand macro="eta0" default_value="1"/> |
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212 <expand macro="warm_start" checked="false"/> |
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213 <expand macro="random_state" default_value="0"/> |
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214 <!--class_weight=None--> |
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215 </section> |
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216 </when> |
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217 </expand> |
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218 </inputs> |
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219 <outputs> |
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220 <data format="tabular" name="outfile_predict"> |
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221 <filter>selected_tasks['selected_task'] == 'load'</filter> |
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222 </data> |
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223 <data format="zip" name="outfile_fit"> |
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224 <filter>selected_tasks['selected_task'] == 'train'</filter> |
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225 </data> |
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226 </outputs> |
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227 <tests> |
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228 <test> |
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229 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> |
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230 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> |
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231 <param name="col1" value="1,2,3,4,5"/> |
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232 <param name="col2" value="6"/> |
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233 <param name="selected_task" value="train"/> |
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234 <param name="selected_algorithm" value="SGDRegressor"/> |
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235 <param name="random_state" value="10"/> |
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236 <output name="outfile_fit" file="glm_model01" compare="sim_size" delta="500"/> |
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237 </test> |
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238 <test> |
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239 <param name="infile_model" value="glm_model01" ftype="zip"/> |
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240 <param name="infile_data" value="regression_test.tabular" ftype="tabular"/> |
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241 <param name="selected_task" value="load"/> |
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242 <output name="outfile_predict" file="glm_result01" compare="sim_size" delta="500"/> |
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243 </test> |
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244 <test> |
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245 <param name="infile1" value="train.tabular" ftype="tabular"/> |
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246 <param name="infile2" value="train.tabular" ftype="tabular"/> |
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247 <param name="col1" value="1,2,3,4"/> |
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248 <param name="col2" value="5"/> |
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249 <param name="selected_task" value="train"/> |
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250 <param name="selected_algorithm" value="SGDClassifier"/> |
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251 <param name="random_state" value="10"/> |
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252 <output name="outfile_fit" file="glm_model02" compare="sim_size" delta="500"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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253 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
254 <test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
255 <param name="infile_model" value="glm_model02" ftype="zip"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
256 <param name="infile_data" value="test.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
257 <param name="selected_task" value="load"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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258 <output name="outfile_predict" file="glm_result02"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
259 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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260 <test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
261 <param name="infile1" value="train.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
262 <param name="infile2" value="train.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
263 <param name="col1" value="1,2,3,4"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
264 <param name="col2" value="5"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
265 <param name="selected_task" value="train"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
266 <param name="selected_algorithm" value="RidgeClassifier"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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267 <param name="random_state" value="10"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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268 <output name="outfile_fit" file="glm_model03" compare="sim_size" delta="500"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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269 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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270 <test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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271 <param name="infile_model" value="glm_model03" ftype="zip"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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272 <param name="infile_data" value="test.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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273 <param name="selected_task" value="load"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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274 <output name="outfile_predict" file="glm_result03"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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275 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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276 <test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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277 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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278 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
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279 <param name="col1" value="1,2,3,4,5"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
280 <param name="col2" value="6"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
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281 <param name="selected_task" value="train"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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282 <param name="selected_algorithm" value="LinearRegression"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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283 <param name="random_state" value="10"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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284 <output name="outfile_fit" file="glm_model04" compare="sim_size" delta="500"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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285 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
286 <test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
287 <param name="infile_model" value="glm_model04" ftype="zip"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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288 <param name="infile_data" value="regression_test.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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289 <param name="selected_task" value="load"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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290 <output name="outfile_predict" file="glm_result04" compare="sim_size"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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291 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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292 <test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
293 <param name="infile1" value="train.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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294 <param name="infile2" value="train.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
295 <param name="col1" value="1,2,3,4"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
296 <param name="col2" value="5"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
297 <param name="selected_task" value="train"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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changeset
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298 <param name="selected_algorithm" value="LogisticRegression"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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299 <param name="random_state" value="10"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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300 <output name="outfile_fit" file="glm_model05" compare="sim_size" delta="500"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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301 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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302 <test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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303 <param name="infile_model" value="glm_model05" ftype="zip"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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304 <param name="infile_data" value="test.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
305 <param name="selected_task" value="load"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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306 <output name="outfile_predict" file="glm_result05"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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307 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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308 <test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
309 <param name="infile1" value="train.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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310 <param name="infile2" value="train.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
311 <param name="col1" value="1,2,3,4"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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312 <param name="col2" value="5"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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313 <param name="selected_task" value="train"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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314 <param name="selected_algorithm" value="LogisticRegressionCV"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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315 <param name="random_state" value="10"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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316 <output name="outfile_fit" file="glm_model06" compare="sim_size" delta="500"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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317 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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318 <test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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319 <param name="infile_model" value="glm_model06" ftype="zip"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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320 <param name="infile_data" value="test.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
321 <param name="selected_task" value="load"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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322 <output name="outfile_predict" file="glm_result06"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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323 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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324 <test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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325 <param name="infile1" value="regression_train.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
326 <param name="infile2" value="regression_train.tabular" ftype="tabular"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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327 <param name="col1" value="1,2,3,4,5"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
328 <param name="col2" value="6"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
|
329 <param name="selected_task" value="train"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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330 <param name="selected_algorithm" value="Ridge"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
|
331 <param name="random_state" value="10"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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332 <output name="outfile_fit" file="glm_model07" compare="sim_size" delta="500"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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333 </test> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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334 <test> |
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335 <param name="infile_model" value="glm_model07" ftype="zip"/> |
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336 <param name="infile_data" value="regression_test.tabular" ftype="tabular"/> |
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337 <param name="selected_task" value="load"/> |
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338 <output name="outfile_predict" file="glm_result07" compare="sim_size"/> |
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339 </test> |
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340 <test> |
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341 <param name="infile1" value="train.tabular" ftype="tabular"/> |
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342 <param name="infile2" value="train.tabular" ftype="tabular"/> |
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343 <param name="col1" value="1,2,3,4"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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344 <param name="col2" value="5"/> |
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345 <param name="selected_task" value="train"/> |
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346 <param name="selected_algorithm" value="LogisticRegressionCV"/> |
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347 <param name="random_state" value="10"/> |
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348 <output name="outfile_fit" file="glm_model08" compare="sim_size" delta="500"/> |
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349 </test> |
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350 <test> |
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351 <param name="infile_model" value="glm_model08" ftype="zip"/> |
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352 <param name="infile_data" value="test.tabular" ftype="tabular"/> |
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353 <param name="selected_task" value="load"/> |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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354 <output name="outfile_predict" file="glm_result08"/> |
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355 </test> |
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356 </tests> |
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357 <help><![CDATA[ |
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358 ***What it does*** |
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359 This module implements a set of linear models for classification and regression such as: SGD classification and regression, Linear and Ridge regression and classification. This wrapper is using sklearn.linear_model module at its core. For information about linear models and their parameter settings please refer to `Scikit-learn generalized linear models`_. |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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360 |
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361 .. _`Scikit-learn generalized linear models`: http://scikit-learn.org/stable/modules/linear_model.html |
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362 |
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363 **1 - Methods** |
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364 There are two groups of operations available: |
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365 |
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366 1 - Train a model : A training set containing samples and their respective labels (or predicted values) are input. Based on the selected algorithm and options, an estimator object is fit to the data and is returned. |
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367 |
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368 2 - Load a model and predict : An existing model predicts the class labels (or regression values) for a new dataset. |
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369 |
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370 **2 - Trainig input** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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371 When you choose to train a model, you need a features dataset X and a labels set y. This tool expects tabular or sparse data for X and a single column for y (tabular). You can select a subset of columns in a tabular dataset as your features dataset or labels column. Below you find some examples: |
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372 |
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373 **Sample tabular features dataset** |
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374 The following training dataset contains 3 feature columns and a column containing class labels. You can simply select the first 3 columns as features and the last column as labels: |
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375 |
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376 :: |
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377 |
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378 4.01163365529 -6.10797684314 8.29829894763 1 |
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379 10.0788438916 1.59539821454 10.0684278289 0 |
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380 -5.17607775503 -0.878286135332 6.92941850665 2 |
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381 4.00975406235 -7.11847496542 9.3802423585 1 |
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382 4.61204065139 -5.71217537352 9.12509610964 1 |
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383 |
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384 |
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385 **Sample sparse features dataset** |
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386 In this case you cannot specifiy a column range. |
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387 |
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388 :: |
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389 |
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390 4 1048577 8738 |
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391 1 271 0.020833 |
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392 1 1038 0.02461 |
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393 2 829017 0.016 |
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394 2 829437 0.012 |
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395 2 830752 0.025 |
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396 3 1047487 0.01 |
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397 3 1047980 0.02 |
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398 3 1048475 0.01 |
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399 4 608 0.016629 |
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400 4 1651 0.02519 |
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401 4 4053 0.04223 |
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402 |
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403 |
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404 **2 - Trainig output** |
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405 The trained model is generated and output in the form of a binary file. |
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406 |
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407 |
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408 **3 - Prediction input** |
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409 |
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410 When you choose to load a model and do prediction, the tool expects an already trained estimator and a tabular dataset as input. The dataset contains new samples which you want to classify or predict regression values for. |
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411 |
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412 |
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413 .. class:: warningmark |
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414 |
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415 The number of feature columns must be the same in training and prediction datasets! |
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416 |
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417 |
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418 **3 - Prediction output** |
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planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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419 The tool predicts the class labels for new samples and adds them as the last column to the prediction dataset. The new dataset then is output as a tabular file. The prediction output format should look like the training dataset. |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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420 |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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changeset
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421 ]]></help> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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422 <expand macro="sklearn_citation"/> |
32a88b3bea94
planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff
changeset
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423 </tool> |