Mercurial > repos > bgruening > sklearn_pairwise_metrics

annotate main_macros.xml @ 0:18afd0c1cc56 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/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
author bgruening
date Wed, 04 May 2016 13:09:52 -0400
parents
children 887b1f85a4b6
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
1 <macros>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
2 <token name="@VERSION@">0.9</token>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
3
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
4 <xml name="python_requirements">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
5 <requirements>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
6 <requirement type="package" version="0.2.1b">eden</requirement>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
7 <yield />
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
8 </requirements>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
9 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
10
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
11 <xml name="macro_stdio">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
12 <stdio>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
13 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
14 </stdio>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
15 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
16
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
17 <xml name="train_loadConditional" token_train="tabular" token_data="tabular" token_model="txt">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
18 <conditional name="selected_tasks">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
19 <param name="selected_task" type="select" label="Select a Classification Task">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
20 <option value="load">Load a model and predict</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
21 <option value="train" selected="true">Train a model</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
22 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
23 <when value="load">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
24 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file." />
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
25 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
26 <conditional name="prediction_options">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
27 <param name="prediction_option" type="select" label="Select the type of prediction">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
28 <option value="predict">Predict class labels</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
29 <option value="advanced">Include advanced options</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
30 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
31 <when value="predict">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
32 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
33 <when value="advanced">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
34 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
35 </conditional>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
36 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
37 <when value="train">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
38 <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)" />
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
39 <conditional name="selected_algorithms">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
40 <yield />
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
41 </conditional>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
42 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
43 </conditional>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
44 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
45
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
46 <xml name="advanced_section">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
47 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
48 <yield />
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
49 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
50 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
51
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
52 <xml name="tabular_input">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
53 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
54 <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
55 <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
56 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
57
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
58 <xml name="tol" token_default_value="0.0" token_help_text="Early stopping heuristics based on the relative center changes. Set to default (0.0) to disable this convergence detection.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
59 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
60 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
61
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
62 <xml name="n_clusters" token_default_value="8">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
63 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
64 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
65
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
66 <xml name="fit_intercept" token_checked="true">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
67 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
68 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
69
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
70 <xml name="n_iter" token_default_value="5" token_help_text="The number of passes over the training data (aka epochs). ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
71 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
72 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
73
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
74 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
75 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
76 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
77
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
78 <xml name="random_state" token_default_value="" token_help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data. A fixed seed allows reproducible results.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
79 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
80 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
81
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
82 <xml name="warm_start" token_checked="true" token_help_text="When set to True, reuse the solution of the previous call to fit as initialization,otherwise, just erase the previous solution.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
83 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
84 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
85
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
86 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
87 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
88 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
89
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
90 <!--xml name="class_weight" token_default_value="" token_help_text="">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
91 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
92 </xml-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
93
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
94 <xml name="alpha" token_default_value="0.0001" token_help_text="Constant that multiplies the regularization term if regularization is used. ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
95 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
96 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
97
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
98 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
99 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
100 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
101
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
102 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
103 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
104 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
105
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
106 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
107 <param argument="noise" type="float" optional="true" value="@DEFAULT_VALUE@" label="Standard deviation of the Gaussian noise added to the data" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
108 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
109
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
110 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
111 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
112 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
113
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
114 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
115 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
116 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
117
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
118 <xml name="n_init" token_default_value="10" >
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
119 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
120 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
121
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
122 <xml name="init">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
123 <param argument="init" type="select" label="Centroid initialization method" help="''k-means++'' selects initial cluster centers that speed up convergence. ''random'' chooses k observations (rows) at random from data as initial centroids.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
124 <option value="k-means++">k-means++</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
125 <option value="random">random</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
126 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
127 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
128
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
129 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
130 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
131 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
132
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
133 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
134 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
135 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
136
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
137 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
138 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
139 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
140
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
141 <xml name="multiple_input" token_name="input_files" token_max_num="10" token_format="txt" token_label="Sparse matrix file (.mtx, .txt)" token_help_text="Specify a sparse matrix file in .txt format.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
142 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
143 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
144 </repeat>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
145 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
146
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
147 <xml name="eden_citation">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
148 <citations>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
149 <citation type="bibtex">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
150 @misc{fabrizio_costa_2015_15094,
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
151 author = {Fabrizio Costa and
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
152 Björn Grüning and
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
153 gigolo},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
154 title = {EDeN: EDeN - Graph Vectorizer},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
155 month = feb,
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
156 year = 2015,
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
157 doi = {10.5281/zenodo.15094},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
158 url = {http://dx.doi.org/10.5281/zenodo.15094}
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
159 }
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
160 }
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
161 </citation>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
162 </citations>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
163 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
164
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
165 <xml name="sklearn_citation">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
166 <citations>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
167 <citation type="bibtex">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
168 @article{scikit-learn,
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
169 title={Scikit-learn: Machine Learning in {P}ython},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
170 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
171 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
172 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
173 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
174 journal={Journal of Machine Learning Research},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
175 volume={12},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
176 pages={2825--2830},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
177 year={2011}
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
178 url = {https://github.com/scikit-learn/scikit-learn}
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
179 }
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
180 </citation>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
181 </citations>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
182 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
183
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
184 <xml name="scipy_citation">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
185 <citations>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
186 <citation type="bibtex">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
187 @Misc{,
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
188 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
189 title = {{SciPy}: Open source scientific tools for {Python}},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
190 year = {2001--},
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
191 url = "http://www.scipy.org/",
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
192 note = {[Online; accessed 2016-04-09]}
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
193 }
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
194 </citation>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
195 </citations>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
196 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
197
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
198
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
199 <xml name="nn_advanced_options">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
200 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
201 <yield/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
202 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
203 <option value="uniform" selected="true" help="Uniform weights. All points in each neighborhood are weighted equally.">Uniform</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
204 <option value="distance" help="Weight points by the inverse of their distance.">Distance</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
205 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
206 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
207 <option value="auto" selected="true">Auto</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
208 <option value="ball_tree">BallTree</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
209 <option value="kd_tree">KDTree</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
210 <option value="brute">Brute-force</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
211 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
212 <param argument="leaf_size" type="integer" value="30" label="Leaf size" help="Used with BallTree and KDTree. Affects the time and memory usage of the constructed tree."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
213 <!--param name="metric"-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
214 <!--param name="p"-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
215 <!--param name="metric_params"-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
216 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
217 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
218
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
219 <xml name="svc_advanced_options">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
220 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
221 <yield/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
222 <param argument="kernel" type="select" optional="true" label="Kernel type" help="Kernel type to be used in the algorithm. If none is given, ‘rbf’ will be used.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
223 <option value="rbf" selected="true">rbf</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
224 <option value="linear">linear</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
225 <option value="poly">poly</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
226 <option value="sigmoid">sigmoid</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
227 <option value="precomputed">precomputed</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
228 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
229 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
230 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
231 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Independent term in kernel function. dafault: 0.0 "/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
232 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use the shrinking heuristic" help=" "/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
233 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
234 <!-- param argument="cache_size"-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
235 <!--expand macro="class_weight"/-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
236 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
237 <expand macro="max_iter" default_value="-1" label="Solver maximum number of iterations" help_text="Hard limit on iterations within solver, or -1 for no limit."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
238 <!--param argument="decision_function_shape"-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
239 <expand macro="random_state" help_text="Integer number. The seed of the pseudo random number generator to use when shuffling the data for probability estimation. A fixed seed allows reproducible results."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
240 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
241 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
242
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
243 <xml name="spectral_clustering_advanced_options">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
244 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
245 <expand macro="n_clusters"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
246 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
247 <option value="arpack" selected="true">arpack</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
248 <option value="lobpcg">lobpcg</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
249 <option value="amg">amg</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
250 <!--None-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
251 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
252 <expand macro="random_state"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
253 <expand macro="n_init"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
254 <param argument="gamma" type="float" optional="true" value="1.0" label="Kernel scaling factor" help="Scaling factor of RBF, polynomial, exponential chi^2 and sigmoid affinity kernel. Ignored for affinity=''nearest_neighbors''."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
255 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
256 <option value="rbf" selected="true">RBF</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
257 <option value="precomputed">precomputed</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
258 <option value="nearest_neighbors">Nearset neighbors</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
259 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
260 <param argument="n_neighbors" type="integer" optional="true" value="10" label="Number of neighbors" help="Number of neighbors to use when constructing the affinity matrix using the nearest neighbors method. Ignored for affinity=''rbf''"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
261 <!--param argument="eigen_tol"-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
262 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
263 <option value="kmeans" selected="true">kmeans</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
264 <option value="discretize">discretize</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
265 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
266 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
267 <param argument="coef0" type="integer" optional="true" value="1" label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
268 <!--param argument="kernel_params"-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
269 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
270 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
271
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
272 <xml name="minibatch_kmeans_advanced_options">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
273 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
274 <expand macro="n_clusters"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
275 <expand macro="init"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
276 <expand macro="n_init" default_value="3"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
277 <expand macro="max_iter" default_value="100"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
278 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
279 <expand macro="random_state"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
280 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
281 <!--param argument="compute_labels"-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
282 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
283 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
284 To disable, set max_no_improvement to None. "/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
285 <param argument="init_size" type="integer" optional="true" value="" label="Number of random initialization samples" help="Number of samples to randomly sample for speeding up the initialization . ( default: 3 * batch_size )"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
286 <param argument="reassignment_ratio" type="float" optional="true" value="0.01" label="Re-assignment ratio" help="Controls the fraction of the maximum number of counts for a center to be reassigned. Higher values yield better clustering results."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
287 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
288 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
289
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
290 <xml name="kmeans_advanced_options">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
291 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
292 <expand macro="n_clusters"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
293 <expand macro="init"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
294 <expand macro="n_init"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
295 <expand macro="max_iter"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
296 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
297 <!--param argument="precompute_distances"/-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
298 <expand macro="random_state"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
299 <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Use a copy of data for precomputing distances" help="Mofifying the original data introduces small numerical differences caused by subtracting and then adding the data mean."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
300 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
301 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
302
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
303 <xml name="birch_advanced_options">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
304 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
305 <param argument="threshold" type="float" optional="true" value="0.5" label="Subcluster radius threshold" help="The radius of the subcluster obtained by merging a new sample; the closest subcluster should be less than the threshold to avoid a new subcluster."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
306 <param argument="branching_factor" type="integer" optional="true" value="50" label="Maximum number of subclusters per branch" help="Maximum number of CF subclusters in each node."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
307 <expand macro="n_clusters" default_value="3"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
308 <!--param argument="compute_labels"/-->
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
309 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
310 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
311
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
312 <xml name="dbscan_advanced_options">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
313 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
314 <param argument="eps" type="float" optional="true" value="0.5" label="Maximum neighborhood distance" help="The maximum distance between two samples for them to be considered as in the same neighborhood."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
315 <param argument="min_samples" type="integer" optional="true" value="5" label="Minimal core point density" help="The number of samples (or total weight) in a neighborhood for a point (including the point itself) to be considered as a core point."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
316 <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."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
317 <param argument="algorithm" type="select" label="Pointwise distance computation algorithm" help="The algorithm to be used by the NearestNeighbors module to compute pointwise distances and find nearest neighbors.">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
318 <option value="auto" selected="true">auto</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
319 <option value="ball_tree">ball_tree</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
320 <option value="kd_tree">kd_tree</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
321 <option value="brute">brute</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
322 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
323 <param argument="leaf_size" type="integer" optional="true" value="30" label="Leaf size" help="Leaf size passed to BallTree or cKDTree. Memory and time efficieny factor in tree constrution and querying."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
324 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
325 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
326
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
327 <xml name="clustering_algorithms_options">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
328 <conditional name="algorithm_options">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
329 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
330 <option value="KMeans" selected="true">KMeans</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
331 <option value="SpectralClustering">Spectral Clustering</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
332 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
333 <option value="DBSCAN">DBSCAN</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
334 <option value="Birch">Birch</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
335 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
336 <when value="KMeans">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
337 <expand macro="kmeans_advanced_options"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
338 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
339 <when value="DBSCAN">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
340 <expand macro="dbscan_advanced_options"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
341 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
342 <when value="Birch">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
343 <expand macro="birch_advanced_options"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
344 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
345 <when value="SpectralClustering">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
346 <expand macro="spectral_clustering_advanced_options"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
347 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
348 <when value="MiniBatchKMeans">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
349 <expand macro="minibatch_kmeans_advanced_options"/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
350 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
351 </conditional>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
352 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
353
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
354 <xml name="distance_metrics">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
355 <param argument="metric" type="select" label="Distance metric" help=" ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
356 <option value="euclidean" selected="true">euclidean</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
357 <option value="cityblock">cityblock</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
358 <option value="cosine">cosine</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
359 <option value="l1">l1</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
360 <option value="l2">l2</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
361 <option value="manhattan">manhattan</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
362 <yield/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
363 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
364 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
365
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
366 <xml name="distance_nonsparse_metrics">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
367 <option value="braycurtis">braycurtis</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
368 <option value="canberra">canberra</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
369 <option value="chebyshev">chebyshev</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
370 <option value="correlation">correlation</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
371 <option value="dice">dice</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
372 <option value="hamming">hamming</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
373 <option value="jaccard">jaccard</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
374 <option value="kulsinski">kulsinski</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
375 <option value="mahalanobis">mahalanobis</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
376 <option value="matching">matching</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
377 <option value="minkowski">minkowski</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
378 <option value="rogerstanimoto">rogerstanimoto</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
379 <option value="russellrao">russellrao</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
380 <option value="seuclidean">seuclidean</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
381 <option value="sokalmichener">sokalmichener</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
382 <option value="sokalsneath">sokalsneath</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
383 <option value="sqeuclidean">sqeuclidean</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
384 <option value="yule">yule</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
385 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
386
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
387 <xml name="pairwise_kernel_metrics">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
388 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
389 <option value="rbf" selected="true">rbf</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
390 <option value="sigmoid">sigmoid</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
391 <option value="polynomial">polynomial</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
392 <option value="linear" selected="true">linear</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
393 <option value="chi2">chi2</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
394 <option value="additive_chi2">additive_chi2</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
395 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
396 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
397
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
398 <xml name="sparse_pairwise_metric_functions">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
399 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
400 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
401 <option value="pairwise_distances">Distance matrix</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
402 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
403 <yield/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
404 </param>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
405 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
406
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
407 <xml name="pairwise_metric_functions">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
408 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
409 <option value="chi2_kernel">Exponential chi-squared kernel</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
410 <option value="linear_kernel">Linear kernel</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
411 <option value="manhattan_distances">L1 distances</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
412 <option value="pairwise_kernels">Kernel</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
413 <option value="polynomial_kernel">Polynomial kernel</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
414 <option value="rbf_kernel">Gaussian (rbf) kernel</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
415 <option value="laplacian_kernel">Laplacian kernel</option>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
416 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
417
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
418 <xml name="sparse_pairwise_condition">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
419 <when value="pairwise_distances">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
420 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
421 <expand macro="distance_metrics">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
422 <yield/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
423 </expand>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
424 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
425 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
426 <when value="euclidean_distances">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
427 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
428 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Return squared Euclidean distances" help=" "/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
429 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
430 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
431 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
432
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
433 <xml name="argmin_distance_condition">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
434 <when value="pairwise_distances_argmin">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
435 <section name="options" title="Advanced Options" expanded="False">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
436 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
437 <expand macro="distance_metrics">
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
438 <yield/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
439 </expand>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
440 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
441 </section>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
442 </when>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
443 </xml>
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
444
18afd0c1cc56 planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 620159e95d2fae693b5f25d591528be159130f25
bgruening
parents:
diff changeset
445 </macros>