Mercurial > repos > bgruening > sklearn_svm_classifier

annotate main_macros.xml @ 26:505d366ad5b2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
author bgruening
date Wed, 09 Aug 2023 14:04:16 +0000
parents b878e4cdd63a
children e92c8a69b0e0
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7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
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1 <macros>
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2 <token name="@VERSION@">1.0.10.0</token>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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3 <token name="@PROFILE@">21.05</token>
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d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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5 <xml name="python_requirements">
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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6 <requirements>
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7 <requirement type="package" version="3.9">python</requirement>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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8 <requirement type="package" version="0.10.0">galaxy-ml</requirement>
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d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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9 <yield />
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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10 </requirements>
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11 </xml>
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d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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13 <xml name="macro_stdio">
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b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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14 <stdio>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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15 <exit_code range=":-1" level="fatal" description="Error occurred. Please check Tool Standard Error" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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16 <exit_code range="137" level="fatal_oom" description="Out of Memory" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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17 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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18 </stdio>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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19 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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21 <!--Generic interface-->
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23 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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24 <conditional name="selected_tasks">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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25 <param name="selected_task" type="select" label="Select a Classification Task">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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26 <option value="train" selected="true">Train a model</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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27 <option value="load">Load a model and predict</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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28 </param>
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29 <when value="load">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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30 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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31 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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32 <param name="header" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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33 <conditional name="prediction_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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34 <param name="prediction_option" type="select" label="Select the type of prediction">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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35 <option value="predict">Predict class labels</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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36 <option value="advanced">Include advanced options</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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37 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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38 <when value="predict">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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39 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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40 <when value="advanced">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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41 </when>
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42 </conditional>
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43 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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44 <when value="train">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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45 <conditional name="selected_algorithms">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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46 <yield />
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47 </conditional>
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48 </when>
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49 </conditional>
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50 </xml>
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51
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52 <xml name="advanced_section">
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53 <section name="options" title="Advanced Options" expanded="False">
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54 <yield />
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55 </section>
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56 </xml>
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59 <!--Generalized Linear Models-->
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60 <xml name="loss" token_help=" " token_select="false">
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61 <param argument="loss" type="select" label="Loss function" help="@HELP@">
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62 <option value="squared_loss" selected="@SELECT@">squared loss</option>
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63 <option value="huber">huber</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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64 <option value="epsilon_insensitive">epsilon insensitive</option>
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65 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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66 <yield />
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67 </param>
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68 </xml>
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69
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70 <xml name="penalty" token_help=" ">
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71 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@">
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72 <option value="l2" selected="true">l2</option>
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73 <option value="l1">l1</option>
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74 <option value="elasticnet">elastic net</option>
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75 <option value="none">none</option>
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76 <yield />
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77 </param>
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78 </xml>
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80 <xml name="l1_ratio" token_default_value="0.15" token_help=" ">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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81 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@" />
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82 </xml>
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84 <xml name="epsilon" token_default_value="0.1" token_help="Used if loss is ‘huber’, ‘epsilon_insensitive’, or ‘squared_epsilon_insensitive’. ">
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85 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@" />
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86 </xml>
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88 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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89 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@">
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90 <option value="optimal" selected="@SELECTED1@">optimal</option>
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91 <option value="constant">constant</option>
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92 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option>
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93 <yield />
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94 </param>
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95 </xml>
0
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96
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97 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. ">
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98 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@" />
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99 </xml>
0
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100
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101 <xml name="power_t" token_default_value="0.5" token_help=" ">
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102 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@" />
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103 </xml>
0
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104
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105 <xml name="normalize" token_checked="false" token_help=" ">
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106 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" " />
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107 </xml>
0
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108
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109 <xml name="copy_X" token_checked="true" token_help=" ">
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110 <param argument="copy_X" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use a copy of samples" help="If false, samples would be overwritten. " />
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111 </xml>
0
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112
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113 <xml name="ridge_params">
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114 <expand macro="normalize" />
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115 <expand macro="alpha" default_value="1.0" />
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116 <expand macro="fit_intercept" />
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117 <expand macro="max_iter" default_value="" />
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118 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. " />
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119 <!--class_weight-->
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120 <expand macro="copy_X" />
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121 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" ">
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122 <option value="auto" selected="true">auto</option>
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123 <option value="svd">svd</option>
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124 <option value="cholesky">cholesky</option>
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125 <option value="lsqr">lsqr</option>
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126 <option value="sparse_cg">sparse_cg</option>
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127 <option value="sag">sag</option>
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128 </param>
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129 <expand macro="random_state" />
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130 </xml>
0
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131
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132 <!--Ensemble methods-->
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133 <xml name="n_estimators" token_default_value="10" token_help=" ">
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134 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@" />
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135 </xml>
0
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136
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137 <xml name="max_depth" token_default_value="" token_help=" ">
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138 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@" />
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139 </xml>
0
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140
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141 <xml name="min_samples_split" token_type="integer" token_default_value="2" token_help=" ">
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142 <param argument="min_samples_split" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@" />
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143 </xml>
0
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144
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145 <xml name="min_samples_leaf" token_type="integer" token_default_value="1" token_label="Minimum number of samples in newly created leaves" token_help=" ">
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146 <param argument="min_samples_leaf" type="@TYPE@" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP@" />
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147 </xml>
0
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148
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149 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
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150 <param argument="min_weight_fraction_leaf" type="float" optional="true" value="@DEFAULT_VALUE@" label="Minimum weighted fraction of the input samples required to be at a leaf node" help="@HELP@" />
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151 </xml>
0
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152
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153 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
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154 <param argument="max_leaf_nodes" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum number of leaf nodes in best-first method" help="@HELP@" />
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155 </xml>
0
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156
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157 <xml name="min_impurity_decrease" token_default_value="0" token_help=" ">
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158 <param argument="min_impurity_decrease" type="float" value="@DEFAULT_VALUE@" optional="true" label="The threshold value of impurity for stopping node splitting" help="@HELP@" />
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159 </xml>
0
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160
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161 <xml name="bootstrap" token_checked="true" token_help=" ">
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162 <param argument="bootstrap" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="@CHECKED@" label="Use bootstrap samples for building trees." help="@HELP@" />
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163 </xml>
0
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164
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165 <xml name="criterion" token_help=" ">
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166 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" ">
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167 <option value="gini" selected="true">Gini impurity</option>
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168 <option value="entropy">Information gain</option>
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169 <yield />
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170 </param>
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171 </xml>
0
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172
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173 <xml name="criterion2" token_help="">
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174 <param argument="criterion" type="select" label="Function to measure the quality of a split" >
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175 <option value="mse">mse - mean squared error</option>
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176 <option value="mae">mae - mean absolute error</option>
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177 <yield />
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178 </param>
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179 </xml>
0
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180
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181 <xml name="oob_score" token_checked="false" token_help=" ">
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182 <param argument="oob_score" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Use out-of-bag samples to estimate the generalization error" help="@HELP@" />
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183 </xml>
0
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184
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185 <xml name="max_features">
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186 <conditional name="select_max_features">
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187 <param argument="max_features" type="select" label="max_features">
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188 <option value="auto" selected="true">auto - max_features=n_features</option>
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189 <option value="sqrt">sqrt - max_features=sqrt(n_features)</option>
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190 <option value="log2">log2 - max_features=log2(n_features)</option>
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191 <option value="number_input">I want to type the number in or input None type</option>
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192 </param>
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193 <when value="auto">
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194 </when>
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195 <when value="sqrt">
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196 </when>
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197 <when value="log2">
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198 </when>
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199 <when value="number_input">
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200 <param name="num_max_features" type="float" value="" optional="true" label="Input max_features number:" help="If int, consider the number of features at each split; If float, then max_features is a percentage and int(max_features * n_features) features are considered at each split." />
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201 </when>
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202 </conditional>
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203 </xml>
0
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204
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205 <xml name="verbose" token_default_value="0" token_help="If 1 then it prints progress and performance once in a while. If greater than 1 then it prints progress and performance for every tree.">
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206 <param argument="verbose" type="integer" value="@DEFAULT_VALUE@" optional="true" label="Enable verbose output" help="@HELP@" />
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207 </xml>
0
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208
25
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209 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
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210 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@" />
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211 </xml>
0
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212
25
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213 <xml name="subsample" token_help=" ">
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214 <param argument="subsample" type="float" value="1.0" optional="true" label="The fraction of samples to be used for fitting the individual base learners" help="@HELP@" />
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215 </xml>
0
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216
25
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217 <xml name="presort">
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218 <param argument="presort" type="select" label="Whether to presort the data to speed up the finding of best splits in fitting" >
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219 <option value="auto" selected="true">auto</option>
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220 <option value="true">true</option>
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221 <option value="false">false</option>
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222 </param>
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223 </xml>
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224
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225 <!-- LightGBM -->
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226 <xml name="feature_fraction" token_help="LightGBM will randomly select part of the features for each iteration (tree) if feature_fraction is smaller than 1.0. For example, if you set it to 0.8, LightGBM will select 80% of features before training each tree.">
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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227 <param argument="feature_fraction" type="float" value="1.0" label="Proportion of features to train each tree" help="@HELP@" />
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228 </xml>
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229
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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230 <xml name="lambda_l1" token_help=" ">
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231 <param argument="lambda_l1" type="float" value="0.0" label="L1 regularization" help="@HELP@" />
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232 </xml>
16
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233
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234 <xml name="lambda_l2" token_help=" ">
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235 <param argument="lambda_l2" type="float" value="0.0" label="L1 regularization" help="@HELP@" />
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236 </xml>
16
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237
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238 <xml name="min_gain_to_split" token_help=" ">
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239 <param argument="min_gain_to_split" type="float" value="0.0" label="Minimal gain to perform split" help="@HELP@" />
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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240 </xml>
16
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241
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242 <xml name="min_child_weight" token_help="Minimal sum hessian in one leaf. It can be used to deal with over-fitting.">
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243 <param argument="min_child_weight" type="float" value="0.0" label="Minimal sum hessian in one leaf" help="@HELP@" />
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244 </xml>
16
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245
25
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246 <!--Parameters-->
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247 <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.">
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248 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@" />
25
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249 </xml>
0
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250
25
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251 <xml name="n_clusters" token_default_value="8">
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252 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" " />
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253 </xml>
0
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254
25
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255 <xml name="fit_intercept" token_checked="true">
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256 <param argument="fit_intercept" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Estimate the intercept" help="If false, the data is assumed to be already centered." />
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257 </xml>
0
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258
25
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259 <xml name="n_iter_no_change" token_default_value="5" token_help_text="Number of iterations with no improvement to wait before early stopping. ">
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260 <param argument="n_iter_no_change" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@" />
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261 </xml>
0
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263 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
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264 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@" />
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265 </xml>
0
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267 <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. default=None.">
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268 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@" />
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269 </xml>
0
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271 <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.">
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272 <param argument="warm_start" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Perform warm start" help="@HELP_TEXT@" />
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273 </xml>
0
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275 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
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276 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@" />
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277 </xml>
0
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279 <!--xml name="class_weight" token_default_value="" token_help_text="">
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280 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@" />
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281 </xml-->
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283 <xml name="alpha" token_default_value="0.0001" token_help_text="Constant that multiplies the regularization term if regularization is used. ">
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284 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@" />
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285 </xml>
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287 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
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288 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@" />
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289 </xml>
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291 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
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292 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@" />
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293 </xml>
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295 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
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296 <param argument="noise" type="float" optional="true" value="@DEFAULT_VALUE@" label="Standard deviation of the Gaussian noise added to the data" help="@HELP_TEXT@" />
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297 </xml>
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299 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
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300 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@" />
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301 </xml>
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303 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
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304 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@" />
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305 </xml>
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307 <xml name="n_init" token_default_value="10" >
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308 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" " />
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309 </xml>
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311 <xml name="init">
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312 <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.">
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313 <option value="k-means++">k-means++</option>
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314 <option value="random">random</option>
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315 </param>
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316 </xml>
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318 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
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319 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@" />
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320 </xml>
0
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321
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322 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
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323 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@" />
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324 </xml>
0
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325
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326 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
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327 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@" />
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328 </xml>
0
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329
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330 <xml name="pos_label" token_default_value="">
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331 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" " />
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332 </xml>
0
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333
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334 <xml name="average">
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335 <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
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336 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option>
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337 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option>
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338 <option value="macro">Calculate metrics for each label, and find their unweighted mean. This does not take label imbalance into account. (macro)</option>
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339 <option value="weighted">Calculate metrics for each label, and find their average, weighted by support (the number of true instances for each label). This alters ‘macro’ to account for label imbalance; it can result in an F-score that is not between precision and recall. (weighted)</option>
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340 <option value="None">None</option>
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341 <yield />
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342 </param>
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343 </xml>
0
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344
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345 <xml name="beta">
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346 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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347 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
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348
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
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349
25
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350 <!--Data interface-->
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351
25
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352 <xml name="samples_tabular" token_label1="Training samples dataset:" token_multiple1="false" token_multiple2="false">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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353 <param name="infile1" type="data" format="tabular" label="@LABEL1@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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354 <param name="header1" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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355 <conditional name="column_selector_options_1">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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356 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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357 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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358 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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359 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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360 <conditional name="column_selector_options_2">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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361 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE2@" infile="infile2" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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362 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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363 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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364 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
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365
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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366 <xml name="samples_column_selector_options" token_column_option="selected_column_selector_option" token_col_name="col1" token_multiple="False" token_infile="infile1">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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367 <param name="@COLUMN_OPTION@" type="select" label="Choose how to select data by column:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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368 <option value="by_index_number" selected="true">Select columns by column index number(s)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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369 <option value="all_but_by_index_number">All columns EXCLUDING some by column index number(s)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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370 <option value="by_header_name">Select columns by column header name(s)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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371 <option value="all_but_by_header_name">All columns EXCLUDING some by column header name(s)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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372 <option value="all_columns">All columns</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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373 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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374 <when value="by_index_number">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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375 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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376 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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377 <when value="all_but_by_index_number">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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378 <param name="@COL_NAME@" multiple="@MULTIPLE@" type="data_column" use_header_names="true" data_ref="@INFILE@" label="Select target column(s):" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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379 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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380 <when value="by_header_name">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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381 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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382 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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383 <when value="all_but_by_header_name">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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384 <param name="@COL_NAME@" type="text" value="" label="Type header name(s):" help="Comma-separated string. For example: target1,target2" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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385 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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386 <when value="all_columns">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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387 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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388 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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389
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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390 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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391 <conditional name="true_columns">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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392 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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393 <option value="tabular" selected="true">Tabular</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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394 <option value="sparse">Sparse</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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395 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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396 <when value="tabular">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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397 <param name="infile1" type="data" label="@LABEL1@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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398 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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399 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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400 <when value="sparse">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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401 <param name="infile1" type="data" format="txt" label="@LABEL1@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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402 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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403 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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404 <conditional name="predicted_columns">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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405 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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406 <option value="tabular" selected="true">Tabular</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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407 <option value="sparse">Sparse</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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408 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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409 <when value="tabular">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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410 <param name="infile2" type="data" label="@LABEL2@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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411 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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412 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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413 <when value="sparse">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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414 <param name="infile2" type="data" format="txt" label="@LABEL1@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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415 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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416 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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417 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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418
25
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419 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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420 <param name="infile1" type="data" format="tabular" label="@LABEL1@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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421 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
422 <conditional name="column_selector_options_1">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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423 <expand macro="samples_column_selector_options" multiple="@MULTIPLE1@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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424 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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425 <param name="infile2" type="data" format="tabular" label="@LABEL2@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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426 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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427 <conditional name="column_selector_options_2">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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428 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="@MULTIPLE@" infile="infile2" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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429 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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430 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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431
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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432 <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.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
433 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
434 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
435 </repeat>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
436 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
437
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
438 <xml name="sparse_target" token_label1="Select a sparse matrix:" token_label2="Select the tabular containing true labels:" token_multiple="False" token_format1="txt" token_format2="tabular" token_help1="" token_help2="">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
439 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
440 <expand macro="input_tabular_target" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
441 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
442
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
443 <xml name="sl_mixed_input">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
444 <conditional name="input_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
445 <expand macro="data_input_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
446 <expand macro="data_input_whens" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
447 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
448 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
449
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
450 <xml name="sl_mixed_input_plus_sequence">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
451 <conditional name="input_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
452 <expand macro="data_input_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
453 <option value="seq_fasta">sequnences in a fasta file</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
454 <option value="refseq_and_interval">reference genome and intervals</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
455 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
456 <expand macro="data_input_whens">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
457 <when value="seq_fasta">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
458 <expand macro="inputs_seq_fasta" />
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
459 </when>
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
460 <when value="refseq_and_interval">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
461 <expand macro="inputs_refseq_and_interval" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
462 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
463 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
464 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
465 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
466
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
467 <xml name="data_input_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
468 <param name="selected_input" type="select" label="Select input type:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
469 <option value="tabular" selected="true">tabular data</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
470 <option value="sparse">sparse matrix</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
471 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
472 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
473 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
474
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
475 <xml name="data_input_whens">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
476 <when value="tabular">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
477 <expand macro="samples_tabular" multiple1="true" multiple2="false" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
478 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
479 <when value="sparse">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
480 <expand macro="sparse_target" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
481 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
482 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
483 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
484
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
485 <xml name="input_tabular_target">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
486 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels or target values:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
487 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
488 <conditional name="column_selector_options_2">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
489 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="false" infile="infile2" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
490 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
491 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
492
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
493 <xml name="inputs_seq_fasta">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
494 <param name="fasta_path" type="data" format="fasta" label="Dataset containing fasta genomic/protein sequences" help="Sequences will be one-hot encoded to arrays." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
495 <expand macro="input_tabular_target" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
496 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
497
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
498 <xml name="inputs_refseq_and_interval">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
499 <param name="ref_genome_file" type="data" format="fasta" label="Dataset containing reference genomic sequence" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
500 <param name="interval_file" type="data" format="interval" label="Dataset containing sequence intervals for training" help="interval. Sequences will be retrieved from the reference genome and one-hot encoded to training arrays." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
501 <param name="target_file" type="data" format="bed" label="Dataset containing positions and features for target values." help="bed. The file will be compressed with `bgzip` and then indexed using `tabix`." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
502 <param name="infile2" type="data" format="tabular" label="Dataset containing the feature list for prediction" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
503 <param name="header2" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Does the dataset contain header:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
504 <conditional name="column_selector_options_2">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
505 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option2" col_name="col2" multiple="true" infile="infile2" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
506 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
507 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
508
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
509 <!--Advanced options-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
510 <xml name="nn_advanced_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
511 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
512 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
513 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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514 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
515 <option value="distance">Weight points by the inverse of their distance. (Distance)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
516 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
517 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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518 <option value="auto" selected="true">Auto</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
519 <option value="ball_tree">BallTree</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
520 <option value="kd_tree">KDTree</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
521 <option value="brute">Brute-force</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
522 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
523 <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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
524 <!--param name="metric"-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
525 <!--param name="p"-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
526 <!--param name="metric_params"-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
527 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
528 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
529
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
530 <xml name="svc_advanced_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
531 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
532 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
533 <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.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
534 <option value="rbf" selected="true">rbf</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
535 <option value="linear">linear</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
536 <option value="poly">poly</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
537 <option value="sigmoid">sigmoid</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
538 <option value="precomputed">precomputed</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
539 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
540 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
541 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
542 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
543 help="Independent term in kernel function. dafault: 0.0 " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
544 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
545 label="Use the shrinking heuristic" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
546 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
547 label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
548 <!-- param argument="cache_size"-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
549 <!--expand macro="class_weight"/-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
550 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
551 <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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
552 <!--param argument="decision_function_shape"-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
553 <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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
554 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
555 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
556
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
557 <xml name="spectral_clustering_advanced_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
558 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
559 <expand macro="n_clusters" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
560 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
561 <option value="arpack" selected="true">arpack</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
562 <option value="lobpcg">lobpcg</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
563 <option value="amg">amg</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
564 <!--None-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
565 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
566 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
567 <expand macro="n_init" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
568 <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''." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
569 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
570 <option value="rbf" selected="true">RBF</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
571 <option value="precomputed">precomputed</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
572 <option value="nearest_neighbors">Nearset neighbors</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
573 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
574 <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''" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
575 <!--param argument="eigen_tol"-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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576 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
577 <option value="kmeans" selected="true">kmeans</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
578 <option value="discretize">discretize</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
579 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
580 <param argument="degree" type="integer" optional="true" value="3"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
581 label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
582 <param argument="coef0" type="integer" optional="true" value="1"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
583 label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
584 <!--param argument="kernel_params"-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
585 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
586 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
587
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
588 <xml name="minibatch_kmeans_advanced_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
589 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
590 <expand macro="n_clusters" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
591 <expand macro="init" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
592 <expand macro="n_init" default_value="3" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
593 <expand macro="max_iter" default_value="100" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
594 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
595 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
596 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
597 <!--param argument="compute_labels"-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
598 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
599 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
600 To disable, set max_no_improvement to None. " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
601 <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 )" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
602 <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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
603 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
604 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
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diff changeset
605
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
606 <xml name="kmeans_advanced_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
607 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
608 <expand macro="n_clusters" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
609 <expand macro="init" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
610 <expand macro="n_init" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
611 <expand macro="max_iter" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
612 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
613 <!--param argument="precompute_distances"/-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
614 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
615 <param argument="copy_x" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" 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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
616 <expand macro="kmeans_algorithm" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
617 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
618 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
619
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
620 <xml name="kmeans_algorithm">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
621 <param argument="algorithm" type="select" label="K-means algorithm to use:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
622 <option value="auto" selected="true">auto</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
623 <option value="full">full</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
624 <option value="elkan">elkan</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
625 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
626 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
627
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
628 <xml name="birch_advanced_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
629 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
630 <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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
631 <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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
632 <expand macro="n_clusters" default_value="3" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
633 <!--param argument="compute_labels"/-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
634 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
635 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
636
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
637 <xml name="dbscan_advanced_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
638 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
639 <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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
640 <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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
641 <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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
642 <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.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
643 <option value="auto" selected="true">auto</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
644 <option value="ball_tree">ball_tree</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
645 <option value="kd_tree">kd_tree</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
646 <option value="brute">brute</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
647 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
648 <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." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
649 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
650 </xml>
10
153f237ddb36 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 9
diff changeset
651
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
652 <xml name="clustering_algorithms_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
653 <conditional name="algorithm_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
654 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
655 <option value="KMeans" selected="true">KMeans</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
656 <option value="SpectralClustering">Spectral Clustering</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
657 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
658 <option value="DBSCAN">DBSCAN</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
659 <option value="Birch">Birch</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
660 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
661 <when value="KMeans">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
662 <expand macro="kmeans_advanced_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
663 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
664 <when value="DBSCAN">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
665 <expand macro="dbscan_advanced_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
666 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
667 <when value="Birch">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
668 <expand macro="birch_advanced_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
669 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
670 <when value="SpectralClustering">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
671 <expand macro="spectral_clustering_advanced_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
672 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
673 <when value="MiniBatchKMeans">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
674 <expand macro="minibatch_kmeans_advanced_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
675 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
676 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
677 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
678
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
679 <xml name="distance_metrics">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
680 <param argument="metric" type="select" label="Distance metric" help=" ">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
681 <option value="euclidean" selected="true">euclidean</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
682 <option value="cityblock">cityblock</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
683 <option value="cosine">cosine</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
684 <option value="l1">l1</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
685 <option value="l2">l2</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
686 <option value="manhattan">manhattan</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
687 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
688 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
689 </xml>
12
73d2ef652879 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 02087ce2966cf8b4aac9197a41171e7f986c11d1-dirty"
bgruening
parents: 11
diff changeset
690
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
691 <xml name="distance_nonsparse_metrics">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
692 <option value="braycurtis">braycurtis</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
693 <option value="canberra">canberra</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
694 <option value="chebyshev">chebyshev</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
695 <option value="correlation">correlation</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
696 <option value="dice">dice</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
697 <option value="hamming">hamming</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
698 <option value="jaccard">jaccard</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
699 <option value="kulsinski">kulsinski</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
700 <option value="mahalanobis">mahalanobis</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
701 <option value="matching">matching</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
702 <option value="minkowski">minkowski</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
703 <option value="rogerstanimoto">rogerstanimoto</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
704 <option value="russellrao">russellrao</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
705 <option value="seuclidean">seuclidean</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
706 <option value="sokalmichener">sokalmichener</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
707 <option value="sokalsneath">sokalsneath</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
708 <option value="sqeuclidean">sqeuclidean</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
709 <option value="yule">yule</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
710 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
711
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
712 <xml name="pairwise_kernel_metrics">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
713 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
714 <option value="rbf" selected="true">rbf</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
715 <option value="sigmoid">sigmoid</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
716 <option value="polynomial">polynomial</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
717 <option value="linear" selected="true">linear</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
718 <option value="chi2">chi2</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
719 <option value="additive_chi2">additive_chi2</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
720 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
721 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
722
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
723 <xml name="sparse_pairwise_metric_functions">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
724 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
725 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
726 <option value="pairwise_distances">Distance matrix</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
727 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
728 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
729 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
730 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
731
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
732 <xml name="pairwise_metric_functions">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
733 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
734 <option value="chi2_kernel">Exponential chi-squared kernel</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
735 <option value="linear_kernel">Linear kernel</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
736 <option value="manhattan_distances">L1 distances</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
737 <option value="pairwise_kernels">Kernel</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
738 <option value="polynomial_kernel">Polynomial kernel</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
739 <option value="rbf_kernel">Gaussian (rbf) kernel</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
740 <option value="laplacian_kernel">Laplacian kernel</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
741 </xml>
10
153f237ddb36 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 60f0fbc0eafd7c11bc60fb6c77f2937782efd8a9-dirty
bgruening
parents: 9
diff changeset
742
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
743 <xml name="sparse_pairwise_condition">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
744 <when value="pairwise_distances">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
745 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
746 <expand macro="distance_metrics">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
747 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
748 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
749 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
750 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
751 <when value="euclidean_distances">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
752 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
753 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
754 label="Return squared Euclidean distances" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
755 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
756 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
757 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
758
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
759 <xml name="argmin_distance_condition">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
760 <when value="pairwise_distances_argmin">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
761 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
762 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
763 <expand macro="distance_metrics">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
764 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
765 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
766 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
767 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
768 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
769 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
770
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
771 <xml name="sparse_preprocessors">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
772 <param name="selected_pre_processor" type="select" label="Select a preprocessor:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
773 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
774 <option value="Binarizer">Binarizer (Binarizes data)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
775 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
776 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
777 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
778 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
779 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
780
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
781 <xml name="sparse_preprocessors_ext">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
782 <expand macro="sparse_preprocessors">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
783 <option value="KernelCenterer">Kernel Centerer (Centers a kernel matrix)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
784 <option value="MinMaxScaler">Minmax Scaler (Scales features to a range)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
785 <option value="PolynomialFeatures">Polynomial Features (Generates polynomial and interaction features)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
786 <option value="RobustScaler">Robust Scaler (Scales features using outlier-invariance statistics)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
787 <option value="QuantileTransformer">QuantileTransformer (Transform features using quantiles information)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
788 <option value="PowerTransformer">PowerTransformer (Apply a power transform featurewise to make data more Gaussian-like)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
789 <option value="KBinsDiscretizer">KBinsDiscretizer (Bin continuous data into intervals.)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
790 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
791 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
792
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
793 <xml name="sparse_preprocessor_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
794 <when value="Binarizer">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
795 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
796 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
797 label="Use a copy of data for precomputing binarization" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
798 <param argument="threshold" type="float" optional="true" value="0.0"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
799 label="Threshold"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
800 help="Feature values below or equal to this are replaced by 0, above it by 1. Threshold may not be less than 0 for operations on sparse matrices. " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
801 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
802 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
803 <when value="StandardScaler">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
804 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
805 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
806 label="Use a copy of data for performing inplace scaling" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
807 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
808 label="Center the data before scaling" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
809 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
810 label="Scale the data to unit variance (or unit standard deviation)" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
811 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
812 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
813 <when value="MaxAbsScaler">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
814 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
815 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
816 label="Use a copy of data for precomputing scaling" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
817 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
818 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
819 <when value="Normalizer">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
820 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
821 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" ">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
822 <option value="l1" selected="true">l1</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
823 <option value="l2">l2</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
824 <option value="max">max</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
825 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
826 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
827 label="Use a copy of data for precomputing row normalization" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
828 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
829 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
830 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
831 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
832
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
833 <xml name="sparse_preprocessor_options_ext">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
834 <expand macro="sparse_preprocessor_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
835 <when value="KernelCenterer">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
836 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
837 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
838 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
839 <when value="MinMaxScaler">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
840 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
841 <param argument="feature_range" type="text" value="(0, 1)" optional="true" help="Desired range of transformed data. None or tuple (min, max). None equals to (0, 1)" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
842 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
843 label="Use a copy of data for precomputing normalization" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
844 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
845 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
846 <when value="PolynomialFeatures">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
847 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
848 <param argument="degree" type="integer" optional="true" value="2" label="The degree of the polynomial features " help="" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
849 <param argument="interaction_only" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="false" label="Produce interaction features only" help="(Features that are products of at most degree distinct input features) " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
850 <param argument="include_bias" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Include a bias column" help="Feature in which all polynomial powers are zero " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
851 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
852 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
853 <when value="RobustScaler">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
854 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
855 <!--=True, =True, copy=True-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
856 <param argument="with_centering" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
857 label="Center the data before scaling" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
858 <param argument="with_scaling" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
859 label="Scale the data to interquartile range" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
860 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
861 label="Use a copy of data for inplace scaling" help=" " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
862 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
863 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
864 <when value="QuantileTransformer">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
865 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
866 <param name="n_quantiles" type="integer" value="1000" min="0" label="Number of quantiles to be computed" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
867 <param name="output_distribution" type="select" label="Marginal distribution for the transformed data">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
868 <option value="uniform" selected="true">uniform</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
869 <option value="normal">normal</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
870 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
871 <param name="ignore_implicit_zeros" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to discard sparse entries" help="Only applies to sparse matrices. If False, sparse entries are treated as zeros" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
872 <param name="subsample" type="integer" value="100000" label="Maximum number of samples used to estimate the quantiles for computational efficiency" help="Note that the subsampling procedure may differ for value-identical sparse and dense matrices." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
873 <expand macro="random_state" help_text="This is used by subsampling and smoothing noise" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
874 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
875 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
876 <when value="PowerTransformer">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
877 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
878 <param name="method" type="select" label="The power transform method">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
879 <option value="yeo-johnson" selected="true">yeo-johnson (works with positive and negative values)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
880 <option value="box-cox">box-cox (might perform better, but only works with strictly positive values)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
881 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
882 <param name="standardize" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Whether to apply zero-mean, unit-variance normalization to the transformed output." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
883 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
884 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
885 <when value="KBinsDiscretizer">
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
886 <section name="options" title="Advanced Options" expanded="False">
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
887 <param name="n_bins" type="integer" value="5" min="2" label="The number of bins to produce" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
888 <param name="encode" type="select" label="Method used to encode the transformed result">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
889 <option value="onehot" selected="true">onehot (encode the transformed result with one-hot encoding and return a sparse matrix)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
890 <option value="onehot-dense">onehot-dense (encode the transformed result with one-hot encoding and return a dense array)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
891 <option value="ordinal">ordinal (return the bin identifier encoded as an integer value)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
892 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
893 <param name="strategy" type="select" label="Strategy used to define the widths of the bins">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
894 <option value="uniform">uniform (all bins in each feature have identical widths)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
895 <option value="quantile" selected="true">quantile (all bins in each feature have the same number of points)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
896 <option value="kmeans">kmeans (values in each bin have the same nearest center of a 1D k-means cluster)</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
897 </param>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
898 </section>
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
899 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
900 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
901 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
902
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
903 <xml name="cv_splitter">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
904 <option value="default" selected="true">default splitter</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
905 <option value="KFold">KFold</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
906 <option value="StratifiedKFold">StratifiedKFold</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
907 <option value="LeaveOneOut">LeaveOneOut</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
908 <option value="LeavePOut">LeavePOut</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
909 <option value="RepeatedKFold">RepeatedKFold</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
910 <option value="RepeatedStratifiedKFold">RepeatedStratifiedKFold</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
911 <option value="ShuffleSplit">ShuffleSplit</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
912 <option value="StratifiedShuffleSplit">StratifiedShuffleSplit</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
913 <option value="TimeSeriesSplit">TimeSeriesSplit</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
914 <option value="PredefinedSplit">PredefinedSplit</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
915 <option value="OrderedKFold">OrderedKFold</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
916 <option value="RepeatedOrderedKFold">RepeatedOrderedKFold</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
917 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
918 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
919
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
920 <xml name="cv_splitter_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
921 <when value="default">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
922 <expand macro="cv_n_splits" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
923 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
924 <when value="KFold">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
925 <expand macro="cv_n_splits" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
926 <expand macro="cv_shuffle" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
927 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
928 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
929 <when value="StratifiedKFold">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
930 <expand macro="cv_n_splits" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
931 <expand macro="cv_shuffle" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
932 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
933 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
934 <when value="LeaveOneOut">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
935 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
936 <when value="LeavePOut">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
937 <param argument="p" type="integer" value="" label="p" help="Integer. Size of the test sets." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
938 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
939 <when value="RepeatedKFold">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
940 <expand macro="cv_n_splits" value="5" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
941 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
942 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
943 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
944 <when value="RepeatedStratifiedKFold">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
945 <expand macro="cv_n_splits" value="5" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
946 <param argument="n_repeats" type="integer" value="10" label="n_repeats" help="Number of times cross-validator needs to be repeated." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
947 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
948 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
949 <when value="ShuffleSplit">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
950 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
951 <expand macro="cv_test_size" value="0.1" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
952 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
953 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
954 <when value="StratifiedShuffleSplit">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
955 <expand macro="cv_n_splits" value="10" help="Number of re-shuffling and splitting iterations." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
956 <expand macro="cv_test_size" value="0.1" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
957 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
958 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
959 <when value="TimeSeriesSplit">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
960 <expand macro="cv_n_splits" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
961 <param argument="max_train_size" type="integer" value="" optional="true" label="Maximum size of the training set" help="Maximum size for a single training set." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
962 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
963 <when value="PredefinedSplit">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
964 <param argument="test_fold" type="text" value="" area="true" label="test_fold" help="List, e.g., [0, 1, -1, 1], represents two test sets, [X[0]] and [X[1], X[3]], X[2] is excluded from any test set due to '-1'." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
965 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
966 <when value="OrderedKFold">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
967 <expand macro="cv_n_splits" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
968 <expand macro="cv_shuffle" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
969 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
970 <expand macro="cv_n_stratification_bins" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
971 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
972 <when value="RepeatedOrderedKFold">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
973 <expand macro="cv_n_splits" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
974 <param argument="n_repeats" type="integer" value="5" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
975 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
976 <expand macro="cv_n_stratification_bins" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
977 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
978 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
979 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
980
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
981 <xml name="cv">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
982 <conditional name="cv_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
983 <param name="selected_cv" type="select" label="Select the cv splitter:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
984 <expand macro="cv_splitter">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
985 <option value="GroupKFold">GroupKFold</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
986 <option value="GroupShuffleSplit">GroupShuffleSplit</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
987 <option value="LeaveOneGroupOut">LeaveOneGroupOut</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
988 <option value="LeavePGroupsOut">LeavePGroupsOut</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
989 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
990 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
991 <expand macro="cv_splitter_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
992 <when value="GroupKFold">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
993 <expand macro="cv_n_splits" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
994 <expand macro="cv_groups" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
995 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
996 <when value="GroupShuffleSplit">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
997 <expand macro="cv_n_splits" value="5" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
998 <expand macro="cv_test_size" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
999 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1000 <expand macro="cv_groups" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1001 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1002 <when value="LeaveOneGroupOut">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1003 <expand macro="cv_groups" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1004 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1005 <when value="LeavePGroupsOut">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1006 <param argument="n_groups" type="integer" value="" label="n_groups" help="Number of groups (p) to leave out in the test split." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1007 <expand macro="cv_groups" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1008 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1009 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1010 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1011 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
1012
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1013 <xml name="cv_reduced" token_label="Select the cv splitter">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1014 <conditional name="cv_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1015 <param name="selected_cv" type="select" label="@LABEL@">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1016 <expand macro="cv_splitter" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1017 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1018 <expand macro="cv_splitter_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1019 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1020 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
1021
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1022 <xml name="cv_n_splits" token_value="5" token_help="Number of folds. Must be at least 2.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1023 <!--why set min to 1?-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1024 <param argument="n_splits" type="integer" value="@VALUE@" min="1" label="n_splits" help="@HELP@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1025 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
1026
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1027 <xml name="cv_shuffle">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1028 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="Whether to shuffle data before splitting" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1029 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
1030
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1031 <xml name="cv_n_stratification_bins">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1032 <param argument="n_stratification_bins" type="integer" value="" optional="true" help="Integer. The number of stratification bins. Only relevent when shuffle is True. Valid in [2, `n_samples // n_splits`]. Default value is None, which is same as `n_samples // n_splits`. The higher the value is, the distribution of target values is more approximately the ame across all split folds." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1033 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1034
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1035 <xml name="cv_test_size" token_value="0.2">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1036 <param argument="test_size" type="float" value="@VALUE@" min="0.0" label="Portion or number of the test set" help="0.0-1.0, proportion of the dataset to include in the test split; >1, integer only, the absolute number of test samples " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1037 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1038
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1039 <xml name="cv_groups" >
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1040 <section name="groups_selector" title="Groups column selector" expanded="true">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1041 <param name="infile_g" type="data" format="tabular" label="Choose dataset containing groups info:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1042 <param name="header_g" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1043 <conditional name="column_selector_options_g">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1044 <expand macro="samples_column_selector_options" column_option="selected_column_selector_option_g" col_name="col_g" multiple="False" infile="infile_g" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1045 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1046 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1047 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1048
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1049 <xml name="train_test_split_params">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1050 <conditional name="split_algos">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1051 <param name="shuffle" type="select" label="Select the splitting method">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1052 <option value="None">No shuffle</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1053 <option value="simple" selected="true">ShuffleSplit</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1054 <option value="stratified">StratifiedShuffleSplit -- target values serve as class labels</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1055 <option value="group">GroupShuffleSplit or split by group names</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1056 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1057 <when value="None">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1058 <expand macro="train_test_split_test_size" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1059 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1060 <when value="simple">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1061 <expand macro="train_test_split_test_size" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1062 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1063 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1064 <when value="stratified">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1065 <expand macro="train_test_split_test_size" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1066 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1067 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1068 <when value="group">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1069 <expand macro="train_test_split_test_size" optional="true" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1070 <expand macro="random_state" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1071 <param argument="group_names" type="text" value="" optional="true" label="Type in group names instead"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1072 help="For example: chr6, chr7. This parameter is optional. If used, it will override the holdout size and random seed." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1073 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1074 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1075 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1076 <!--param argument="train_size" type="float" optional="True" value="" label="Train size:" />-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1077 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1078
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1079 <xml name="train_test_split_test_size" token_optional="false">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1080 <param name="test_size" type="float" value="0.2" optional="@OPTIONAL@" label="Holdout size" help="Leass than 1, for preportion; greater than 1 (integer), for number of samples." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1081 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1082
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1083 <xml name="feature_selection_algorithms">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1084 <option value="SelectKBest" selected="true">SelectKBest - Select features according to the k highest scores</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1085 <option value="GenericUnivariateSelect">GenericUnivariateSelect - Univariate feature selector with configurable strategy</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1086 <option value="SelectPercentile">SelectPercentile - Select features according to a percentile of the highest scores</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1087 <option value="SelectFpr">SelectFpr - Filter: Select the p-values below alpha based on a FPR test</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1088 <option value="SelectFdr">SelectFdr - Filter: Select the p-values for an estimated false discovery rate</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1089 <option value="SelectFwe">SelectFwe - Filter: Select the p-values corresponding to Family-wise error rate</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1090 <option value="VarianceThreshold">VarianceThreshold - Feature selector that removes all low-variance features</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1091 <option value="SelectFromModel">SelectFromModel - Meta-transformer for selecting features based on importance weights</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1092 <option value="RFE">RFE - Feature ranking with recursive feature elimination</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1093 <option value="RFECV">RFECV - Feature ranking with recursive feature elimination and cross-validated selection of the best number of features</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1094 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1095 </xml>
7
372582a7a34d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 5
diff changeset
1096
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1097 <xml name="feature_selection_algorithm_details">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1098 <when value="GenericUnivariateSelect">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1099 <expand macro="feature_selection_score_function" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1100 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1101 <param argument="mode" type="select" label="Feature selection mode">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1102 <option value="percentile">percentile</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1103 <option value="k_best">k_best</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1104 <option value="fpr">fpr</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1105 <option value="fdr">fdr</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1106 <option value="fwe">fwe</option>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
1107 </param>
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1108 <param argument="param" type="float" value="" optional="true" label="Parameter of the corresponding mode" help="float or int depending on the feature selection mode" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1109 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1110 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1111 <when value="SelectPercentile">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1112 <expand macro="feature_selection_score_function" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1113 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1114 <param argument="percentile" type="integer" value="10" optional="True" label="Percent of features to keep" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1115 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1116 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1117 <when value="SelectKBest">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1118 <expand macro="feature_selection_score_function" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1119 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1120 <param argument="k" type="integer" value="10" optional="True" label="Number of top features to select" help="No 'all' option is supported." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1121 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1122 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1123 <when value="SelectFpr">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1124 <expand macro="feature_selection_score_function" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1125 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1126 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest p-value for features to be kept." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1127 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1128 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1129 <when value="SelectFdr">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1130 <expand macro="feature_selection_score_function" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1131 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1132 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1133 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1134 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1135 <when value="SelectFwe">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1136 <expand macro="feature_selection_score_function" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1137 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1138 <param argument="alpha" type="float" value="" optional="True" label="Alpha" help="The highest uncorrected p-value for features to keep." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1139 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1140 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1141 <when value="VarianceThreshold">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1142 <section name="options" title="Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1143 <param argument="threshold" type="float" value="0.0" optional="True" label="Threshold" help="Features with a training-set variance lower than this threshold will be removed." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1144 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1145 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1146 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
1147
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1148 <xml name="feature_selection_SelectFromModel">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1149 <when value="SelectFromModel">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1150 <conditional name="model_inputter">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1151 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?" >
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1152 <option value="new" selected="true">Yes</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1153 <option value="prefitted">No. Load a prefitted estimator</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1154 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1155 <when value="new">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1156 <expand macro="estimator_selector_fs" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1157 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1158 <when value="prefitted">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1159 <param name="fitted_estimator" type="data" format='h5mlm' label="Load a prefitted estimator" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1160 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1161 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1162 <expand macro="feature_selection_SelectFromModel_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1163 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1164 </xml>
3
297541cc26d0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 2
diff changeset
1165
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1166 <xml name="feature_selection_SelectFromModel_no_prefitted">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1167 <when value="SelectFromModel">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1168 <conditional name="model_inputter">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1169 <param name="input_mode" type="select" label="Construct a new estimator from a selection list?" >
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1170 <option value="new" selected="true">Yes</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1171 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1172 <when value="new">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1173 <expand macro="estimator_selector_all" />
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
1174 </when>
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1175 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1176 <expand macro="feature_selection_SelectFromModel_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1177 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1178 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1179
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1180 <xml name="feature_selection_SelectFromModel_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1181 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1182 <param argument="threshold" type="text" value="" optional="true" label="threshold" help="The threshold value to use for feature selection. e.g. 'mean', 'median', '1.25*mean'." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1183 <param argument="norm_order" type="integer" value="1" label="norm_order" help="Order of the norm used to filter the vectors of coefficients below threshold in the case where the coef_ attribute of the estimator is of dimension 2. " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1184 <param argument="max_features" type="integer" value="" optional="true" label="The maximum number of features selected scoring above threshold" help="To disable threshold and only select based on max_features, set threshold=-np.inf." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1185 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1186 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1187
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1188 <xml name="feature_selection_RFE">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1189 <when value="RFE">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1190 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1191 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1192 <param argument="n_features_to_select" type="integer" value="" optional="true" label="n_features_to_select" help="The number of features to select. If None, half of the features are selected." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1193 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1194 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1195 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1196 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1197 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1198
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1199 <xml name="feature_selection_RFECV_fs">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1200 <when value="RFECV">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1201 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1202 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1203 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1204 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1205 <expand macro="cv" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1206 <expand macro="scoring_selection" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1207 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1208 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1209 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1210 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1211
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1212 <xml name="feature_selection_RFECV_pipeline">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1213 <when value="RFECV">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1214 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1215 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1216 <param argument="step" type="float" value="1" label="step" optional="true" help="Default = 1. " />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1217 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1218 <expand macro="cv_reduced" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1219 <!-- TODO: group splitter support-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1220 <expand macro="scoring_selection" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1221 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1222 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1223 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1224 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1225
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1226 <xml name="feature_selection_DyRFECV_fs">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1227 <when value="DyRFECV">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1228 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1229 <section name="options" title="Advanced Options" expanded="False">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1230 <param argument="step" type="text" size="30" value="1" label="step" optional="true" help="Default = 1. Support float, int and list." >
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1231 <sanitizer>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1232 <valid initial="default">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1233 <add value="[" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1234 <add value="]" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1235 </valid>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1236 </sanitizer>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1237 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1238 <param argument="min_features_to_select" type="integer" value="1" optional="true" label="The minimum number of features to be selected" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1239 <expand macro="cv" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1240 <expand macro="scoring_selection" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1241 <param argument="verbose" type="integer" value="0" label="verbose" help="Controls verbosity of output." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1242 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1243 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1244 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1245
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1246 <xml name="feature_selection_pipeline">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1247 <!--compare to `feature_selection_fs`, no fitted estimator for SelectFromModel and no custom estimator for RFE and RFECV-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1248 <conditional name="fs_algorithm_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1249 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1250 <expand macro="feature_selection_algorithms" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1251 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1252 <expand macro="feature_selection_algorithm_details" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1253 <expand macro="feature_selection_SelectFromModel_no_prefitted" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1254 <expand macro="feature_selection_RFE">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1255 <expand macro="estimator_selector_all" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1256 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1257 <expand macro="feature_selection_RFECV_pipeline">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1258 <expand macro="estimator_selector_all" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1259 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1260 <!-- TODO: add DyRFECV to pipeline-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1261 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1262 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1263
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1264 <xml name="feature_selection_fs">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1265 <conditional name="fs_algorithm_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1266 <param name="selected_algorithm" type="select" label="Select a feature selection algorithm">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1267 <expand macro="feature_selection_algorithms">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1268 <option value="DyRFECV">DyRFECV - Extended RFECV with changeable steps</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1269 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1270 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1271 <expand macro="feature_selection_algorithm_details" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1272 <expand macro="feature_selection_SelectFromModel" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1273 <expand macro="feature_selection_RFE">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1274 <expand macro="estimator_selector_fs" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1275 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1276 <expand macro="feature_selection_RFECV_fs">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1277 <expand macro="estimator_selector_fs" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1278 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1279 <expand macro="feature_selection_DyRFECV_fs">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1280 <expand macro="estimator_selector_fs" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1281 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1282 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1283 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1284
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1285 <xml name="feature_selection_score_function">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1286 <param argument="score_func" type="select" label="Select a score function">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1287 <option value="chi2">chi2 - Compute chi-squared stats between each non-negative feature and class</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1288 <option value="f_classif">f_classif - Compute the ANOVA F-value for the provided sample</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1289 <option value="f_regression">f_regression - Univariate linear regression tests</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1290 <option value="mutual_info_classif">mutual_info_classif - Estimate mutual information for a discrete target variable</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1291 <option value="mutual_info_regression">mutual_info_regression - Estimate mutual information for a continuous target variable</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1292 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1293 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1294
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1295 <xml name="model_validation_common_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1296 <expand macro="cv" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1297 <expand macro="verbose" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1298 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1299 </xml>
7
372582a7a34d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 5
diff changeset
1300
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1301 <xml name="scoring_selection" token_help="Metric to refit the best estimator.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1302 <conditional name="scoring">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1303 <param name="primary_scoring" type="select" multiple="false" label="Select the primary metric (scoring):" help="@HELP@">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1304 <option value="default" selected="true">default with estimator</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1305 <expand macro="scoring_selection_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1306 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1307 <when value="default" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1308 <when value="accuracy"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1309 <when value="balanced_accuracy"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1310 <when value="average_precision"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1311 <when value="f1"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1312 <when value="f1_micro"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1313 <when value="f1_macro"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1314 <when value="f1_weighted"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1315 <when value="f1_samples"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1316 <when value="neg_log_loss"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1317 <when value="precision"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1318 <when value="precision_micro"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1319 <when value="precision_macro"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1320 <when value="precision_wighted"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1321 <when value="precision_samples"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1322 <when value="recall"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1323 <when value="recall_micro"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1324 <when value="recall_macro"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1325 <when value="recall_wighted"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1326 <when value="recall_samples"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1327 <when value="roc_auc"><expand macro="secondary_scoring_selection_classification" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1328 <when value="explained_variance"><expand macro="secondary_scoring_selection_regression" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1329 <when value="neg_mean_absolute_error"><expand macro="secondary_scoring_selection_regression" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1330 <when value="neg_mean_squared_error"><expand macro="secondary_scoring_selection_regression" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1331 <when value="neg_mean_squared_log_error"><expand macro="secondary_scoring_selection_regression" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1332 <when value="neg_median_absolute_error"><expand macro="secondary_scoring_selection_regression" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1333 <when value="r2"><expand macro="secondary_scoring_selection_regression" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1334 <when value="max_error"><expand macro="secondary_scoring_selection_regression" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1335 <when value="spearman_correlation"><expand macro="secondary_scoring_selection_regression" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1336 <when value="binarize_auc_scorer"><expand macro="secondary_scoring_selection_anormaly" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1337 <when value="binarize_average_precision_scorer"><expand macro="secondary_scoring_selection_anormaly" /></when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1338 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1339 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
1340
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1341 <xml name="scoring_selection_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1342 <option value="accuracy">Classification -- 'accuracy'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1343 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1344 <option value="average_precision">Classification -- 'average_precision'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1345 <option value="f1">Classification -- 'f1'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1346 <option value="f1_micro">Classification -- 'f1_micro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1347 <option value="f1_macro">Classification -- 'f1_macro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1348 <option value="f1_weighted">Classification -- 'f1_weighted'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1349 <option value="f1_samples">Classification -- 'f1_samples'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1350 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1351 <option value="precision">Classification -- 'precision'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1352 <option value="precision_micro">Classification -- 'precision_micro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1353 <option value="precision_macro">Classification -- 'precision_macro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1354 <option value="precision_wighted">Classification -- 'precision_wighted'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1355 <option value="precision_samples">Classification -- 'precision_samples'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1356 <option value="recall">Classification -- 'recall'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1357 <option value="recall_micro">Classification -- 'recall_micro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1358 <option value="recall_macro">Classification -- 'recall_macro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1359 <option value="recall_wighted">Classification -- 'recall_wighted'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1360 <option value="recall_samples">Classification -- 'recall_samples'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1361 <option value="roc_auc">Classification -- 'roc_auc'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1362 <option value="explained_variance">Regression -- 'explained_variance'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1363 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1364 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1365 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1366 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1367 <option value="r2">Regression -- 'r2'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1368 <option value="max_error">Regression -- 'max_error'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1369 <option value="spearman_correlation">Regression -- Spearman's rank correlation coefficient</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1370 <option value="binarize_auc_scorer">anomaly detection -- binarize_auc_scorer</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1371 <option value="binarize_average_precision_scorer">anomaly detection -- binarize_average_precision_scorer</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1372 </xml>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
1373
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1374 <xml name="secondary_scoring_selection_classification">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1375 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1376 <option value="accuracy">Classification -- 'accuracy'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1377 <option value="balanced_accuracy">Classification -- 'balanced_accuracy'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1378 <option value="average_precision">Classification -- 'average_precision'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1379 <option value="f1">Classification -- 'f1'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1380 <option value="f1_micro">Classification -- 'f1_micro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1381 <option value="f1_macro">Classification -- 'f1_macro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1382 <option value="f1_weighted">Classification -- 'f1_weighted'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1383 <option value="f1_samples">Classification -- 'f1_samples'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1384 <option value="neg_log_loss">Classification -- 'neg_log_loss'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1385 <option value="precision">Classification -- 'precision'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1386 <option value="precision_micro">Classification -- 'precision_micro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1387 <option value="precision_macro">Classification -- 'precision_macro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1388 <option value="precision_wighted">Classification -- 'precision_wighted'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1389 <option value="precision_samples">Classification -- 'precision_samples'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1390 <option value="recall">Classification -- 'recall'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1391 <option value="recall_micro">Classification -- 'recall_micro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1392 <option value="recall_macro">Classification -- 'recall_macro'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1393 <option value="recall_wighted">Classification -- 'recall_wighted'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1394 <option value="recall_samples">Classification -- 'recall_samples'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1395 <option value="roc_auc">Classification -- 'roc_auc'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1396 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1397 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1398
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1399 <xml name="secondary_scoring_selection_regression">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1400 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1401 <option value="explained_variance">Regression -- 'explained_variance'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1402 <option value="neg_mean_absolute_error">Regression -- 'neg_mean_absolute_error'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1403 <option value="neg_mean_squared_error">Regression -- 'neg_mean_squared_error'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1404 <option value="neg_mean_squared_log_error">Regression -- 'neg_mean_squared_log_error'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1405 <option value="neg_median_absolute_error">Regression -- 'neg_median_absolute_error'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1406 <option value="r2">Regression -- 'r2'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1407 <option value="max_error">Regression -- 'max_error'</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1408 <option value="spearman_correlation">Regression -- Spearman's rank correlation coefficient</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1409 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1410 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1411
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1412 <xml name="secondary_scoring_selection_anormaly">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1413 <param name="secondary_scoring" type="select" multiple="true" label="Additional scoring used in multi-metric mode:" help="If the same metric with the primary is chosen, the metric will be ignored.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1414 <expand macro="scoring_selection_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1415 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1416 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1417
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1418 <xml name="pre_dispatch" token_type="hidden" token_default_value="all" token_help="Number of predispatched jobs for parallel execution">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1419 <param argument="pre_dispatch" type="@TYPE@" value="@DEFAULT_VALUE@" optional="true" label="pre_dispatch" help="@HELP@" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1420 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1421
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1422 <xml name="estimator_and_hyperparameter">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1423 <param name="infile_estimator" type="data" format="h5mlm" label="Choose the dataset containing pipeline/estimator object" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1424 <section name="hyperparams_swapping" title="Hyperparameter Swapping" expanded="false">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1425 <repeat name="param_set" min="1" max="30" title="New hyperparameter setting">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1426 <param name="sp_name" type="select" optional="true" label="Choose a parameter name (with current value)">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1427 <options from_dataset="infile_estimator" meta_file_key="hyper_params" startswith="@">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1428 <column name="name" index="2" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1429 <column name="value" index="1" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1430 <filter type="unique_value" name="unique_param" column="1" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1431 </options>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1432 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1433 <param name="sp_value" type="text" value="" optional="true" label="New value" help="Supports int, float, boolean, single quoted string, and selected object constructor. Similar to the `Parameter settings for search` section in `searchcv` tool except that only single value is expected here.">
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
1434 <sanitizer>
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1435 <valid initial="default">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1436 <add value="&apos;" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1437 <add value="&quot;" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1438 </valid>
19
d67dcd63f6cb "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 17
diff changeset
1439 </sanitizer>
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1440 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1441 </repeat>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1442 </section>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1443 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
1444
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1445 <xml name="search_cv_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1446 <expand macro="scoring_selection" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1447 <expand macro="model_validation_common_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1448 <!--expand macro="pre_dispatch" default_value="2*n_jobs" help="Controls the number of jobs that get dispatched during parallel execution"/-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1449 <!--param argument="iid" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="iid" help="If True, data is identically distributed across the folds" />-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1450 <!--param argument="refit" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="refit" help="Refit an estimator using the best found parameters on the whole dataset. Be aware that `refit=True` invokes extra computation, but it's REQUIRED for outputting the best estimator!" /> -->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1451 <param argument="error_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" label="Raise fit error:" help="If false, the metric score is assigned to NaN if an error occurs in estimator fitting and FitFailedWarning is raised." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1452 <param argument="return_train_score" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="false" label="return_train_score" help="" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1453 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
1454
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1455 <xml name="estimator_module_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1456 <option value="svm" selected="true">sklearn.svm</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1457 <option value="linear_model">sklearn.linear_model</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1458 <option value="ensemble">sklearn.ensemble</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1459 <option value="naive_bayes">sklearn.naive_bayes</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1460 <option value="tree">sklearn.tree</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1461 <option value="neighbors">sklearn.neighbors</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1462 <option value="xgboost">xgboost</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1463 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1464 </xml>
3
297541cc26d0 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit d00173591e4a783a4c1cb2664e4bb192ab5414f7
bgruening
parents: 2
diff changeset
1465
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1466 <xml name="estimator_suboptions">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1467 <when value="svm">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1468 <param name="selected_estimator" type="select" label="Choose estimator class:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1469 <option value="LinearSVC" selected="true">LinearSVC</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1470 <option value="LinearSVR">LinearSVR</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1471 <option value="NuSVC">NuSVC</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1472 <option value="NuSVR">NuSVR</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1473 <option value="OneClassSVM">OneClassSVM</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1474 <option value="SVC">SVC</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1475 <option value="SVR">SVR</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1476 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1477 <expand macro="estimator_params_text" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1478 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1479 <when value="linear_model">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1480 <param name="selected_estimator" type="select" label="Choose estimator class:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1481 <option value="ARDRegression" selected="true">ARDRegression</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1482 <option value="BayesianRidge">BayesianRidge</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1483 <option value="ElasticNet">ElasticNet</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1484 <option value="ElasticNetCV">ElasticNetCV</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1485 <option value="HuberRegressor">HuberRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1486 <option value="Lars">Lars</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1487 <option value="LarsCV">LarsCV</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1488 <option value="Lasso">Lasso</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1489 <option value="LassoCV">LassoCV</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1490 <option value="LassoLars">LassoLars</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1491 <option value="LassoLarsCV">LassoLarsCV</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1492 <option value="LassoLarsIC">LassoLarsIC</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1493 <option value="LinearRegression">LinearRegression</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1494 <option value="LogisticRegression">LogisticRegression</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1495 <option value="LogisticRegressionCV">LogisticRegressionCV</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1496 <option value="MultiTaskLasso">MultiTaskLasso</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1497 <option value="MultiTaskElasticNet">MultiTaskElasticNet</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1498 <option value="MultiTaskLassoCV">MultiTaskLassoCV</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1499 <option value="MultiTaskElasticNetCV">MultiTaskElasticNetCV</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1500 <option value="OrthogonalMatchingPursuit">OrthogonalMatchingPursuit</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1501 <option value="OrthogonalMatchingPursuitCV">OrthogonalMatchingPursuitCV</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1502 <option value="PassiveAggressiveClassifier">PassiveAggressiveClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1503 <option value="PassiveAggressiveRegressor">PassiveAggressiveRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1504 <option value="Perceptron">Perceptron</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1505 <option value="RANSACRegressor">RANSACRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1506 <option value="Ridge">Ridge</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1507 <option value="RidgeClassifier">RidgeClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1508 <option value="RidgeClassifierCV">RidgeClassifierCV</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1509 <option value="RidgeCV">RidgeCV</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1510 <option value="SGDClassifier">SGDClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1511 <option value="SGDRegressor">SGDRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1512 <option value="TheilSenRegressor">TheilSenRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1513 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1514 <expand macro="estimator_params_text" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1515 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1516 <when value="ensemble">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1517 <param name="selected_estimator" type="select" label="Choose estimator class:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1518 <option value="AdaBoostClassifier" selected="true">AdaBoostClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1519 <option value="AdaBoostRegressor">AdaBoostRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1520 <option value="BaggingClassifier">BaggingClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1521 <option value="BaggingRegressor">BaggingRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1522 <option value="ExtraTreesClassifier">ExtraTreesClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1523 <option value="ExtraTreesRegressor">ExtraTreesRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1524 <option value="GradientBoostingClassifier">GradientBoostingClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1525 <option value="GradientBoostingRegressor">GradientBoostingRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1526 <option value="IsolationForest">IsolationForest</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1527 <option value="HistGradientBoostingClassifier">HistGradientBoostingClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1528 <option value="HistGradientBoostingRegressor">HistGradientBoostingRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1529 <option value="RandomForestClassifier">RandomForestClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1530 <option value="RandomForestRegressor">RandomForestRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1531 <option value="RandomTreesEmbedding">RandomTreesEmbedding</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1532 <!--option value="VotingClassifier">VotingClassifier</option-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1533 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1534 <expand macro="estimator_params_text" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1535 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1536 <when value="naive_bayes">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1537 <param name="selected_estimator" type="select" label="Choose estimator class:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1538 <option value="BernoulliNB" selected="true">BernoulliNB</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1539 <option value="GaussianNB">GaussianNB</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1540 <option value="MultinomialNB">MultinomialNB</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1541 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1542 <expand macro="estimator_params_text" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1543 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1544 <when value="tree">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1545 <param name="selected_estimator" type="select" label="Choose estimator class:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1546 <option value="DecisionTreeClassifier" selected="true">DecisionTreeClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1547 <option value="DecisionTreeRegressor">DecisionTreeRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1548 <option value="ExtraTreeClassifier">ExtraTreeClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1549 <option value="ExtraTreeRegressor">ExtraTreeRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1550 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1551 <expand macro="estimator_params_text" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1552 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1553 <when value="neighbors">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1554 <param name="selected_estimator" type="select" label="Choose estimator class:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1555 <option value="KNeighborsClassifier" selected="true">KNeighborsClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1556 <option value="KNeighborsRegressor">KNeighborsRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1557 <!--option value="BallTree">BallTree</option-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1558 <!--option value="KDTree">KDTree</option-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1559 <option value="KernelDensity">KernelDensity</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1560 <option value="LocalOutlierFactor">LocalOutlierFactor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1561 <option value="RadiusNeighborsClassifier">RadiusNeighborsClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1562 <option value="RadiusNeighborsRegressor">RadiusNeighborsRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1563 <option value="NearestCentroid">NearestCentroid</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1564 <option value="NearestNeighbors">NearestNeighbors</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1565 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1566 <expand macro="estimator_params_text" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1567 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1568 <when value="xgboost">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1569 <param name="selected_estimator" type="select" label="Choose estimator class:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1570 <option value="XGBRegressor" selected="true">XGBRegressor</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1571 <option value="XGBClassifier">XGBClassifier</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1572 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1573 <expand macro="estimator_params_text" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1574 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1575 <yield />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1576 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1577
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1578 <xml name="estimator_selector_all">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1579 <conditional name="estimator_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1580 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1581 <expand macro="estimator_module_options" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1582 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1583 <expand macro="estimator_suboptions" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1584 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1585 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1586
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1587 <xml name="estimator_selector_fs">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1588 <conditional name="estimator_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1589 <param name="selected_module" type="select" label="Choose the module that contains target estimator:" >
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1590 <expand macro="estimator_module_options">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1591 <option value="custom_estimator">Load a custom estimator</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1592 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1593 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1594 <expand macro="estimator_suboptions">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1595 <when value="custom_estimator">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1596 <param name="c_estimator" type="data" format="h5mlm" label="Choose the dataset containing the custom estimator or pipeline:" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1597 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1598 </expand>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1599 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1600 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1601
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1602 <xml name="estimator_params_text" token_label="Type in parameter settings if different from default:" token_default_value=''
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1603 token_help="Dictionary-capable, e.g., C=1, kernel='linear'. No double quotes. Leave this box blank for default estimator.">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1604 <param name="text_params" type="text" value="@DEFAULT_VALUE@" optional="true" label="@LABEL@" help="@HELP@">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1605 <sanitizer>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1606 <valid initial="default">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1607 <add value="&apos;" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1608 </valid>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1609 </sanitizer>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1610 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1611 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1612
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1613 <xml name="kernel_approximation_all">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1614 <conditional name="kernel_approximation_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1615 <param name="select_algorithm" type="select" label="Choose a kernel approximation algorithm:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1616 <option value="Nystroem" selected="true">Nystroem</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1617 <option value="RBFSampler">RBFSampler</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1618 <option value="AdditiveChi2Sampler">AdditiveChi2Sampler</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1619 <option value="SkewedChi2Sampler">SkewedChi2Sampler</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1620 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1621 <when value="Nystroem">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1622 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1623 help="Default(=blank): coef0=None, degree=None, gamma=None, kernel='rbf', kernel_params=None, n_components=100, random_state=None. No double quotes" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1624 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1625 <when value="RBFSampler">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1626 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1627 help="Default(=blank): gamma=1.0, n_components=100, random_state=None." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1628 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1629 <when value="AdditiveChi2Sampler">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1630 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1631 help="Default(=blank): sample_interval=None, sample_steps=2." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1632 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1633 <when value="SkewedChi2Sampler">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1634 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1635 help="Default(=blank): n_components=100, random_state=None, skewedness=1.0." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1636 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1637 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1638 </xml>
7
372582a7a34d planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 5
diff changeset
1639
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1640 <xml name="matrix_decomposition_all">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1641 <conditional name="matrix_decomposition_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1642 <param name="select_algorithm" type="select" label="Choose a matrix decomposition algorithm:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1643 <option value="DictionaryLearning" selected="true">DictionaryLearning</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1644 <option value="FactorAnalysis">FactorAnalysis</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1645 <option value="FastICA">FastICA</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1646 <option value="IncrementalPCA">IncrementalPCA</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1647 <option value="KernelPCA">KernelPCA</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1648 <option value="LatentDirichletAllocation">LatentDirichletAllocation</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1649 <option value="MiniBatchDictionaryLearning">MiniBatchDictionaryLearning</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1650 <option value="MiniBatchSparsePCA">MiniBatchSparsePCA</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1651 <option value="NMF">NMF</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1652 <option value="PCA">PCA</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1653 <option value="SparsePCA">SparsePCA</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1654 <!--option value="SparseCoder">SparseCoder</option-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1655 <option value="TruncatedSVD">TruncatedSVD</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1656 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1657 <when value="DictionaryLearning">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1658 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1659 help="Default(=blank): alpha=1, code_init=None, dict_init=None, fit_algorithm='lars', max_iter=1000, n_components=None, random_state=None, split_sign=False, tol=1e-08, transform_algorithm='omp', transform_alpha=None, transform_n_nonzero_coefs=None, verbose=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1660 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1661 <when value="FactorAnalysis">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1662 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1663 help="Default(=blank): copy=True, iterated_power=3, max_iter=1000, n_components=None, noise_variance_init=None, random_state=0, svd_method='randomized', tol=0.01." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1664 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1665 <when value="FastICA">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1666 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1667 help="Default(=blank): algorithm='parallel', fun='logcosh', fun_args=None, max_iter=200, n_components=None, random_state=None, tol=0.0001, w_init=None, whiten=True. No double quotes." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1668 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1669 <when value="IncrementalPCA">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1670 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1671 help="Default(=blank): batch_size=None, copy=True, n_components=None, whiten=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1672 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1673 <when value="KernelPCA">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1674 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1675 help="Default(=blank): alpha=1.0, coef0=1, copy_X=True, degree=3, eigen_solver='auto', fit_inverse_transform=False, gamma=None, kernel='linear', kernel_params=None, max_iter=None, n_components=None, random_state=None, remove_zero_eig=False, tol=0. No double quotes." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1676 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1677 <when value="LatentDirichletAllocation">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1678 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1679 help="Default(=blank): batch_size=128, doc_topic_prior=None, evaluate_every=-1, learning_decay=0.7, learning_method=None, learning_offset=10.0, max_doc_update_iter=100, max_iter=10, mean_change_tol=0.001, n_components=10, n_topics=None, perp_tol=0.1, random_state=None, topic_word_prior=None, total_samples=1000000.0, verbose=0." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1680 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1681 <when value="MiniBatchDictionaryLearning">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1682 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1683 help="Default(=blank): alpha=1, batch_size=3, dict_init=None, fit_algorithm='lars', n_components=None, n_iter=1000, random_state=None, shuffle=True, split_sign=False, transform_algorithm='omp', transform_alpha=None, transform_n_nonzero_coefs=None, verbose=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1684 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1685 <when value="MiniBatchSparsePCA">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1686 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1687 help="Default(=blank): alpha=1, batch_size=3, callback=None, method='lars', n_components=None, n_iter=100, random_state=None, ridge_alpha=0.01, shuffle=True, verbose=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1688 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1689 <when value="NMF">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1690 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1691 help="Default(=blank): alpha=0.0, beta_loss='frobenius', init=None, l1_ratio=0.0, max_iter=200, n_components=None, random_state=None, shuffle=False, solver='cd', tol=0.0001, verbose=0." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1692 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1693 <when value="PCA">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1694 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1695 help="Default(=blank): copy=True, iterated_power='auto', n_components=None, random_state=None, svd_solver='auto', tol=0.0, whiten=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1696 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1697 <when value="SparsePCA">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1698 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1699 help="Default(=blank): U_init=None, V_init=None, alpha=1, max_iter=1000, method='lars', n_components=None, random_state=None, ridge_alpha=0.01, tol=1e-08, verbose=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1700 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1701 <when value="TruncatedSVD">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1702 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1703 help="Default(=blank): algorithm='randomized', n_components=2, n_iter=5, random_state=None, tol=0.0." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1704 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1705 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1706 </xml>
8
1a9d5a8fff12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
1707
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1708 <xml name="FeatureAgglomeration">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1709 <conditional name="FeatureAgglomeration_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1710 <param name="select_algorithm" type="select" label="Choose the algorithm:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1711 <option value="FeatureAgglomeration" selected="true">FeatureAgglomeration</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1712 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1713 <when value="FeatureAgglomeration">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1714 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1715 help="Default(=blank): affinity='euclidean', compute_full_tree='auto', connectivity=None, linkage='ward', memory=None, n_clusters=2, pooling_func=np.mean." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1716 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1717 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1718 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1719
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1720 <xml name="skrebate">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1721 <conditional name="skrebate_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1722 <param name="select_algorithm" type="select" label="Choose the algorithm:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1723 <option value="ReliefF">ReliefF</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1724 <option value="SURF">SURF</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1725 <option value="SURFstar">SURFstar</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1726 <option value="MultiSURF">MultiSURF</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1727 <option value="MultiSURFstar">MultiSURFstar</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1728 <!--option value="TuRF">TuRF</option> -->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1729 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1730 <when value="ReliefF">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1731 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1732 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, n_neighbors=100, verbose=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1733 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1734 <when value="SURF">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1735 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1736 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1737 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1738 <when value="SURFstar">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1739 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1740 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1741 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1742 <when value="MultiSURF">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1743 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1744 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1745 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1746 <when value="MultiSURFstar">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1747 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1748 help="Default(=blank): discrete_threshold=10, n_features_to_select=10, verbose=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1749 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1750 <!--when value="TuRF">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1751 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1752 help="Default(=blank): core_algorithm='ReliefF', discrete_threshold=10, n_features_to_select=10, n_neighbors=100, pct=0.5, verbose=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1753 </when> -->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1754 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1755 </xml>
8
1a9d5a8fff12 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
bgruening
parents: 7
diff changeset
1756
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1757 <xml name="imbalanced_learn_sampling">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1758 <conditional name="imblearn_selector">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1759 <param name="select_algorithm" type="select" label="Choose the algorithm:">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1760 <option value="under_sampling.ClusterCentroids" selected="true">under_sampling.ClusterCentroids</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1761 <option value="under_sampling.CondensedNearestNeighbour">under_sampling.CondensedNearestNeighbour</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1762 <option value="under_sampling.EditedNearestNeighbours">under_sampling.EditedNearestNeighbours</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1763 <option value="under_sampling.RepeatedEditedNearestNeighbours">under_sampling.RepeatedEditedNearestNeighbours</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1764 <option value="under_sampling.AllKNN">under_sampling.AllKNN</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1765 <option value="under_sampling.InstanceHardnessThreshold">under_sampling.InstanceHardnessThreshold</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1766 <option value="under_sampling.NearMiss">under_sampling.NearMiss</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1767 <option value="under_sampling.NeighbourhoodCleaningRule">under_sampling.NeighbourhoodCleaningRule</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1768 <option value="under_sampling.OneSidedSelection">under_sampling.OneSidedSelection</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1769 <option value="under_sampling.RandomUnderSampler">under_sampling.RandomUnderSampler</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1770 <option value="under_sampling.TomekLinks">under_sampling.TomekLinks</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1771 <option value="over_sampling.ADASYN">over_sampling.ADASYN</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1772 <option value="over_sampling.RandomOverSampler">over_sampling.RandomOverSampler</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1773 <option value="over_sampling.SMOTE">over_sampling.SMOTE</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1774 <option value="over_sampling.SVMSMOTE">over_sampling.SVMSMOTE</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1775 <option value="over_sampling.BorderlineSMOTE">over_sampling.BorderlineSMOTE</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1776 <option value="over_sampling.SMOTENC">over_sampling.SMOTENC</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1777 <option value="combine.SMOTEENN">combine.SMOTEENN</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1778 <option value="combine.SMOTETomek">combine.SMOTETomek</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1779 <option value="Z_RandomOverSampler">Z_RandomOverSampler - for regression</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1780 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1781 <when value="under_sampling.ClusterCentroids">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1782 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1783 help="Default(=blank): sampling_strategy='auto', random_state=None, estimator=None, voting='auto'." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1784 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1785 <when value="under_sampling.CondensedNearestNeighbour">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1786 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1787 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=None, n_seeds_S=1." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1788 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1789 <when value="under_sampling.EditedNearestNeighbours">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1790 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1791 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, max_iter=100, kind_sel='all'." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1792 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1793 <when value="under_sampling.RepeatedEditedNearestNeighbours">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1794 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1795 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, max_iter=100, kind_sel='all'." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1796 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1797 <when value="under_sampling.AllKNN">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1798 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1799 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, kind_sel='all', allow_minority=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1800 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1801 <when value="under_sampling.InstanceHardnessThreshold">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1802 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1803 help="Default(=blank): estimator=None, sampling_strategy='auto', random_state=None, cv=5." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1804 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1805 <when value="under_sampling.NearMiss">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1806 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1807 help="Default(=blank): sampling_strategy='auto', random_state=None, version=1, n_neighbors=3, n_neighbors_ver3=3." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1808 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1809 <when value="under_sampling.NeighbourhoodCleaningRule">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1810 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1811 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=3, kind_sel='all', threshold_cleaning=0.5." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1812 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1813 <when value="under_sampling.OneSidedSelection">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1814 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1815 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=None, n_seeds_S=1." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1816 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1817 <when value="under_sampling.RandomUnderSampler">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1818 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1819 help="Default(=blank): sampling_strategy='auto', random_state=None, replacement=False." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1820 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1821 <when value="under_sampling.TomekLinks">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1822 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1823 help="Default(=blank): sampling_strategy='auto', random_state=None." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1824 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1825 <when value="over_sampling.ADASYN">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1826 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1827 help="Default(=blank): sampling_strategy='auto', random_state=None, n_neighbors=5." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1828 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1829 <when value="over_sampling.RandomOverSampler">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1830 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1831 help="Default(=blank): sampling_strategy='auto', random_state=None." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1832 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1833 <when value="over_sampling.SMOTE">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1834 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1835 help="Default(=blank): sampling_strategy='auto', random_state=None, k_neighbors=5." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1836 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1837 <when value="over_sampling.SVMSMOTE">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1838 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1839 help="Default(=blank): sampling_strategy='auto', k_neighbors=5, m_neighbors=10, out_step=0.5, random_state=None, svm_estimator=None." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1840 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1841 <when value="over_sampling.BorderlineSMOTE">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1842 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1843 help="Default(=blank): sampling_strategy='auto', k_neighbors=5, kind='borderline-1', m_neighbors=10, random_state=None." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1844 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1845 <when value="over_sampling.SMOTENC">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1846 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1847 help="Default: categorical_features=[], sampling_strategy='auto', random_state=None, k_neighbors=5." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1848 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1849 <when value="combine.SMOTEENN">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1850 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1851 help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, enn=None." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1852 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1853 <when value="combine.SMOTETomek">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1854 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1855 help="Default(=blank): sampling_strategy='auto', random_state=None, smote=None, tomek=None." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1856 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1857 <when value="Z_RandomOverSampler">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1858 <expand macro="estimator_params_text"
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1859 help="Default(=blank): sampling_strategy='auto', random_state=None, negative_thres=0, positive_thres=-1." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1860 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1861 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1862 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
1863
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1864 <xml name="preprocessors_sequence_encoders">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1865 <conditional name="encoder_selection">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1866 <param name="encoder_type" type="select" label="Choose the sequence encoder class">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1867 <option value="GenomeOneHotEncoder">GenomeOneHotEncoder</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1868 <option value="ProteinOneHotEncoder">ProteinOneHotEncoder</option>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1869 </param>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1870 <when value="GenomeOneHotEncoder">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1871 <expand macro="preprocessors_sequence_encoder_arguments" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1872 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1873 <when value="ProteinOneHotEncoder">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1874 <expand macro="preprocessors_sequence_encoder_arguments" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1875 </when>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1876 </conditional>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1877 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
1878
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1879 <xml name="preprocessors_sequence_encoder_arguments">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1880 <param argument="seq_length" type="integer" value="" min="0" optional="true" help="Integer. Sequence length" />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1881 <param argument="padding" type="boolean" truevalue="booltrue" falsevalue="boolfalse" checked="true" help="Whether to pad or truncate sequence to meet the sequence length." />
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1882 </xml>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1883
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1884 <!-- Outputs -->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1885
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1886 <xml name="output">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1887 <outputs>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1888 <data format="tabular" name="outfile_predict">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1889 <filter>selected_tasks['selected_task'] == 'load'</filter>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1890 </data>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1891 <data format="h5mlm" name="outfile_fit" label="${tool.name}.${selected_tasks.selected_algorithms.selected_algorithm}">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1892 <filter>selected_tasks['selected_task'] == 'train'</filter>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1893 </data>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1894 </outputs>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1895 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
1896
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1897 <!--Citations-->
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1898 <xml name="eden_citation">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1899 <citations>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1900 <citation type="doi">10.5281/zenodo.15094</citation>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1901 </citations>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1902 </xml>
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
bgruening
parents:
diff changeset
1903
25
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1904 <xml name="sklearn_citation">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1905 <citations>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1906 <citation type="bibtex">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1907 @article{scikit-learn,
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1908 title={Scikit-learn: Machine Learning in {P}ython},
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1909 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1910 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1911 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
diff changeset
1912 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
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1913 journal={Journal of Machine Learning Research},
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1914 volume={12},
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1915 pages={2825--2830},
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1916 year={2011}
0
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1917 }
25
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1918 </citation>
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1919 <yield />
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1920 </citations>
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1921 </xml>
0
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diff changeset
1922
25
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1923 <xml name="scipy_citation">
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1924 <citations>
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1925 <citation type="bibtex">
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1926 @Misc{,
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1927 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
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1928 title = {{SciPy}: Open source scientific tools for {Python}},
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1929 year = {2001--},
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1930 url = "http://www.scipy.org/",
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1931 note = {[Online; accessed 2016-04-09]}
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1932 }
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1933 </citation>
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1934 </citations>
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1935 </xml>
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parents: 24
diff changeset
1936
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parents: 24
diff changeset
1937 <xml name="skrebate_citation">
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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1938 <citation type="bibtex">
4
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1939 @article{DBLP:journals/corr/abs-1711-08477,
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parents: 3
diff changeset
1940 author = {Ryan J. Urbanowicz and
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parents: 3
diff changeset
1941 Randal S. Olson and
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parents: 3
diff changeset
1942 Peter Schmitt and
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parents: 3
diff changeset
1943 Melissa Meeker and
41d0edb7d1fc planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cf3d813ec755166ee0bd517b4ecbbd4f84d4df1
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parents: 3
diff changeset
1944 Jason H. Moore},
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parents: 3
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1945 title = {Benchmarking Relief-Based Feature Selection Methods},
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parents: 3
diff changeset
1946 journal = {CoRR},
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parents: 3
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1947 volume = {abs/1711.08477},
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parents: 3
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1948 year = {2017},
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parents: 3
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1949 url = {http://arxiv.org/abs/1711.08477},
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parents: 3
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1950 archivePrefix = {arXiv},
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1951 eprint = {1711.08477},
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parents: 3
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1952 timestamp = {Mon, 13 Aug 2018 16:46:04 +0200},
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parents: 3
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1953 biburl = {https://dblp.org/rec/bib/journals/corr/abs-1711-08477},
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parents: 3
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1954 bibsource = {dblp computer science bibliography, https://dblp.org}
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parents: 3
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1955 }
25
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1956 </citation>
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1957 </xml>
4
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parents: 3
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1958
25
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1959 <xml name="xgboost_citation">
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1960 <citation type="bibtex">
4
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parents: 3
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1961 @inproceedings{Chen:2016:XST:2939672.2939785,
25
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parents: 24
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1962 author = {Chen, Tianqi and Guestrin, Carlos},
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parents: 24
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1963 title = {{XGBoost}: A Scalable Tree Boosting System},
4
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1964 booktitle = {Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining},
25
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1965 series = {KDD '16},
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parents: 24
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1966 year = {2016},
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1967 isbn = {978-1-4503-4232-2},
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parents: 24
diff changeset
1968 location = {San Francisco, California, USA},
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parents: 24
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1969 pages = {785--794},
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parents: 24
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1970 numpages = {10},
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1971 url = {http://doi.acm.org/10.1145/2939672.2939785},
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parents: 24
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1972 doi = {10.1145/2939672.2939785},
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1973 acmid = {2939785},
4
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1974 publisher = {ACM},
25
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parents: 24
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1975 address = {New York, NY, USA},
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1976 keywords = {large-scale machine learning},
4
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1977 }
25
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diff changeset
1978 </citation>
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1979 </xml>
4
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parents: 3
diff changeset
1980
25
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parents: 24
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1981 <xml name="imblearn_citation">
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1982 <citation type="bibtex">
7
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parents: 5
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1983 @article{JMLR:v18:16-365,
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parents: 5
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1984 author = {Guillaume Lema{{\^i}}tre and Fernando Nogueira and Christos K. Aridas},
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1985 title = {Imbalanced-learn: A Python Toolbox to Tackle the Curse of Imbalanced Datasets in Machine Learning},
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parents: 5
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1986 journal = {Journal of Machine Learning Research},
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parents: 5
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1987 year = {2017},
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parents: 5
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1988 volume = {18},
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parents: 5
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1989 number = {17},
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parents: 5
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1990 pages = {1-5},
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1991 url = {http://jmlr.org/papers/v18/16-365.html}
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parents: 5
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1992 }
25
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1993 </citation>
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1994 </xml>
7
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parents: 5
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1995
25
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diff changeset
1996 <xml name="selene_citation">
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parents: 24
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1997 <citation type="bibtex">
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diff changeset
1998 @article{chen2019selene,
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diff changeset
1999 title={Selene: a PyTorch-based deep learning library for sequence data},
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parents: 24
diff changeset
2000 author={Chen, Kathleen M and Cofer, Evan M and Zhou, Jian and Troyanskaya, Olga G},
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parents: 24
diff changeset
2001 journal={Nature methods},
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parents: 24
diff changeset
2002 volume={16},
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parents: 24
diff changeset
2003 number={4},
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parents: 24
diff changeset
2004 pages={315},
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
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2005 year={2019},
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 24
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2006 publisher={Nature Publishing Group}
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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parents: 24
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2007 }
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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parents: 24
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2008 </citation>
b878e4cdd63a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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parents: 24
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2009 </xml>
10
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bgruening
parents: 9
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2010
0
7bee4014724a planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 8cbb681224f23fa95783514f949c97d6c2c60966
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2011 </macros>