Mercurial > repos > bgruening > sklearn_nn_classifier

annotate nn_classifier.xml @ 32:fdd27282ed8e draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
author bgruening
date Fri, 03 Nov 2023 22:41:56 +0000
parents 22f0b9db4ea1
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
27
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
1 <tool id="sklearn_nn_classifier" name="Nearest Neighbors Classification" version="@VERSION@" profile="@PROFILE@">
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
2 <description></description>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
3 <macros>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
4 <import>main_macros.xml</import>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
5 </macros>
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
6 <expand macro="python_requirements" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
7 <expand macro="macro_stdio" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
8 <version_command>echo "@VERSION@"</version_command>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
9 <command><![CDATA[
2
c4ed38067415 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 2afd4f6be8b2870c2b3701189b28111bfa3ca0ad
bgruening
parents: 1
diff changeset
10 python '$nnc_script' '$inputs'
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
11 ]]>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
12 </command>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
13 <configfiles>
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
14 <inputs name="inputs" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
15 <configfile name="nnc_script">
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
16 <![CDATA[
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
17 import sys
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
18 import json
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
19 import numpy as np
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
20 import sklearn.neighbors
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
21 import pandas
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
22
27
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
23 from galaxy_ml.model_persist import dump_model_to_h5, load_model_from_h5
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
24 from galaxy_ml.utils import clean_params, get_X_y
12
d0efc68a3ddb planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 10
diff changeset
25
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
26
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
27 input_json_path = sys.argv[1]
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
28 with open(input_json_path, "r") as param_handler:
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
29 params = json.load(param_handler)
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
30
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
31 #if $selected_tasks.selected_task == "load":
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
32
27
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
33 classifier_object = load_model_from_h5('$infile_model')
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
34 classifier_object = clean_params(classifier_object)
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
35
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
36 header = 'infer' if params["selected_tasks"]["header"] else None
17
699024d5c451 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5b2ac730ec6d3b762faa9034eddd19ad1b347476"
bgruening
parents: 12
diff changeset
37 data = pandas.read_csv("$selected_tasks.infile_data", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None)
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
38 prediction = classifier_object.predict(data)
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
39 prediction_df = pandas.DataFrame(prediction)
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
40 res = pandas.concat([data, prediction_df], axis=1)
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
41 res.to_csv(path_or_buf = "$outfile_predict", sep="\t", index=False)
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
42
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
43 #else:
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
44
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
45 X, y = get_X_y(params, "$selected_tasks.selected_algorithms.input_options.infile1" ,"$selected_tasks.selected_algorithms.input_options.infile2")
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
46
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
47 selected_algorithm = params["selected_tasks"]["selected_algorithms"]["selected_algorithm"]
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
48
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
49 if selected_algorithm == "nneighbors":
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
50 classifier = params["selected_tasks"]["selected_algorithms"]["sampling_methods"]["sampling_method"]
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
51 sys.stdout.write(classifier)
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
52 options = params["selected_tasks"]["selected_algorithms"]["sampling_methods"]["options"]
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
53 sys.stdout.write(str(options))
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
54 elif selected_algorithm == "ncentroid":
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
55 options = params["selected_tasks"]["selected_algorithms"]["options"]
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
56 classifier = "NearestCentroid"
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
57
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
58 my_class = getattr(sklearn.neighbors, classifier)
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
59 classifier_object = my_class(**options)
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
60 classifier_object.fit(X, y)
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
61
27
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
62 dump_model_to_h5(classifier_object, '$outfile_fit')
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
63
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
64 #end if
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
65
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
66 ]]>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
67 </configfile>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
68 </configfiles>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
69 <inputs>
27
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
70 <expand macro="sl_Conditional" model="h5mlm"> <!--Todo: add sparse to targets-->
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
71 <param name="selected_algorithm" type="select" label="Classifier type">
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
72 <option value="nneighbors">Nearest Neighbors</option>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
73 <option value="ncentroid">Nearest Centroid</option>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
74 </param>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
75 <when value="nneighbors">
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
76 <expand macro="sl_mixed_input" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
77 <conditional name="sampling_methods">
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
78 <param name="sampling_method" type="select" label="Neighbor selection method">
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
79 <option value="KNeighborsClassifier" selected="true">K-nearest neighbors</option>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
80 <option value="RadiusNeighborsClassifier">Radius-based</option>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
81 </param>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
82 <when value="KNeighborsClassifier">
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
83 <expand macro="nn_advanced_options">
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
84 <param argument="n_neighbors" type="integer" optional="true" value="5" label="Number of neighbors" help=" " />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
85 </expand>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
86 </when>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
87 <when value="RadiusNeighborsClassifier">
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
88 <expand macro="nn_advanced_options">
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
89 <param argument="radius" type="float" optional="true" value="1.0" label="Radius" help="Range of parameter space to use by default for :meth ''radius_neighbors'' queries." />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
90 </expand>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
91 </when>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
92 </conditional>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
93 </when>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
94 <when value="ncentroid">
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
95 <expand macro="sl_mixed_input" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
96 <section name="options" title="Advanced Options" expanded="False">
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
97 <param argument="metric" type="text" optional="true" value="euclidean" label="Metric" help="The metric to use when calculating distance between instances in a feature array." />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
98 <param argument="shrink_threshold" type="float" optional="true" value="" label="Shrink threshold" help="Floating point number for shrinking centroids to remove features." />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
99 </section>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
100 </when>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
101 </expand>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
102 </inputs>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
103
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
104 <expand macro="output" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
105
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
106 <tests>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
107 <test>
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
108 <param name="infile1" value="train_set.tabular" ftype="tabular" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
109 <param name="infile2" value="train_set.tabular" ftype="tabular" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
110 <param name="header1" value="True" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
111 <param name="header2" value="True" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
112 <param name="col1" value="1,2,3,4" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
113 <param name="col2" value="5" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
114 <param name="selected_task" value="train" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
115 <param name="selected_algorithm" value="nneighbors" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
116 <param name="sampling_method" value="KNeighborsClassifier" />
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
117 <param name="algorithm" value="brute" />
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
118 <output name="outfile_fit" file="nn_model01" compare="sim_size" delta="5" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
119 </test>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
120 <test>
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
121 <param name="infile1" value="train_set.tabular" ftype="tabular" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
122 <param name="infile2" value="train_set.tabular" ftype="tabular" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
123 <param name="header1" value="True" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
124 <param name="header2" value="True" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
125 <param name="col1" value="1,2,3,4" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
126 <param name="col2" value="5" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
127 <param name="selected_task" value="train" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
128 <param name="selected_algorithm" value="nneighbors" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
129 <param name="sampling_method" value="RadiusNeighborsClassifier" />
27
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
130 <param name="algorithm" value="brute" />
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
131 <output name="outfile_fit" file="nn_model02" compare="sim_size" delta="5" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
132 </test>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
133 <test>
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
134 <param name="infile1" value="train_set.tabular" ftype="tabular" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
135 <param name="infile2" value="train_set.tabular" ftype="tabular" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
136 <param name="header1" value="True" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
137 <param name="header2" value="True" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
138 <param name="col1" value="1,2,3,4" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
139 <param name="col2" value="5" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
140 <param name="selected_task" value="train" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
141 <param name="selected_algorithm" value="ncentroid" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
142 <output name="outfile_fit" file="nn_model03" compare="sim_size" delta="5" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
143 </test>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
144 <test>
27
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
145 <param name="infile_model" value="nn_model01" ftype="h5mlm" />
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
146 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
147 <param name="header" value="True" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
148 <param name="selected_task" value="load" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
149 <output name="outfile_predict" file="nn_prediction_result01.tabular" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
150 </test>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
151 <test>
27
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
152 <param name="infile_model" value="nn_model02" ftype="h5mlm" />
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
153 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
154 <param name="header" value="True" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
155 <param name="selected_task" value="load" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
156 <output name="outfile_predict" file="nn_prediction_result02.tabular" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
157 </test>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
158 <test>
27
22f0b9db4ea1 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 21
diff changeset
159 <param name="infile_model" value="nn_model03" ftype="h5mlm" />
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
160 <param name="infile_data" value="test_set.tabular" ftype="tabular" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
161 <param name="header" value="True" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
162 <param name="selected_task" value="load" />
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
163 <output name="outfile_predict" file="nn_prediction_result03.tabular" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
164 </test>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
165 </tests>
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
166 <help><![CDATA[
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
167 **What it does**
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
168 This module implements the k-nearest neighbors classification algorithms.
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
169 For more information check http://scikit-learn.org/stable/modules/neighbors.html
21
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
170 ]]> </help>
1d3447c2203c "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
171 <expand macro="sklearn_citation" />
0
b7d0fc23bfe4 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
172 </tool>