annotate main_macros.xml @ 4:24485b92adf5 draft

planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit cea052cf3b8dd4f3620253bd222e126de32e7466
author bgruening
date Thu, 22 Mar 2018 13:45:44 -0400
parents bf0ea4cece8b
children fce83b4979a1
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dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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1 <macros>
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2 <token name="@VERSION@">0.9</token>
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3
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4 <token name="@COLUMNS_FUNCTION@">
2
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5 def read_columns(f, c, **args):
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6 data = pandas.read_csv(f, **args)
0
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7 cols = c.split (',')
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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8 cols = map(int, cols)
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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9 cols = list(map(lambda x: x - 1, cols))
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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10 y = data.iloc[:,cols].values
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11 return y
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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12 </token>
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13
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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14 <xml name="python_requirements">
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15 <requirements>
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16 <requirement type="package" version="2.7">python</requirement>
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17 <requirement type="package" version="0.19.1">scikit-learn</requirement>
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18 <requirement type="package" version="0.22.0">pandas</requirement>
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19 <yield />
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20 </requirements>
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21 </xml>
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22
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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23 <xml name="macro_stdio">
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24 <stdio>
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25 <exit_code range="1:" level="fatal" description="Error occurred. Please check Tool Standard Error"/>
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26 </stdio>
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27 </xml>
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28
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29
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30 <!--Generic interface-->
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31 <xml name="train_loadConditional" token_train="tabular" token_data="tabular" token_model="txt">
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32 <conditional name="selected_tasks">
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33 <param name="selected_task" type="select" label="Select a Classification Task">
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34 <option value="train" selected="true">Train a model</option>
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35 <option value="load">Load a model and predict</option>
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36 </param>
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37 <when value="load">
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38 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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39 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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40 <conditional name="prediction_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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41 <param name="prediction_option" type="select" label="Select the type of prediction">
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42 <option value="predict">Predict class labels</option>
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43 <option value="advanced">Include advanced options</option>
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44 </param>
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45 <when value="predict">
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46 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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47 <when value="advanced">
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48 </when>
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49 </conditional>
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50 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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51 <when value="train">
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52 <param name="infile_train" type="data" format="@TRAIN@" label="Training samples (tabular)"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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53 <conditional name="selected_algorithms">
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54 <yield />
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55 </conditional>
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56 </when>
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57 </conditional>
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58 </xml>
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59
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60 <xml name="sl_Conditional" token_train="tabular" token_data="tabular" token_model="txt">
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61 <conditional name="selected_tasks">
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62 <param name="selected_task" type="select" label="Select a Classification Task">
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63 <option value="train" selected="true">Train a model</option>
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64 <option value="load">Load a model and predict</option>
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65 </param>
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66 <when value="load">
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67 <param name="infile_model" type="data" format="@MODEL@" label="Models" help="Select a model file."/>
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68 <param name="infile_data" type="data" format="@DATA@" label="Data (tabular)" help="Select the dataset you want to classify."/>
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69 <conditional name="prediction_options">
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70 <param name="prediction_option" type="select" label="Select the type of prediction">
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71 <option value="predict">Predict class labels</option>
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72 <option value="advanced">Include advanced options</option>
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73 </param>
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74 <when value="predict">
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75 </when>
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76 <when value="advanced">
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77 </when>
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78 </conditional>
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79 </when>
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80 <when value="train">
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81 <conditional name="selected_algorithms">
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82 <yield />
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83 </conditional>
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84 </when>
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85 </conditional>
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86 </xml>
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87
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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88 <xml name="advanced_section">
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89 <section name="options" title="Advanced Options" expanded="False">
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90 <yield />
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91 </section>
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92 </xml>
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93
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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94
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95 <!--Generalized Linear Models-->
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96 <xml name="loss" token_help=" " token_select="false">
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97 <param argument="loss" type="select" label="Loss function" help="@HELP@">
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98 <option value="squared_loss" selected="@SELECT@">squared loss</option>
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99 <option value="huber">huber</option>
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100 <option value="epsilon_insensitive">epsilon insensitive</option>
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101 <option value="squared_epsilon_insensitive">squared epsilon insensitive</option>
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102 <yield/>
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103 </param>
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104 </xml>
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105
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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106 <xml name="penalty" token_help=" ">
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107 <param argument="penalty" type="select" label="Penalty (regularization term)" help="@HELP@">
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108 <option value="l2" selected="true">l2</option>
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109 <option value="l1">l1</option>
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110 <option value="elasticnet">elastic net</option>
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111 <option value="none">none</option>
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112 <yield/>
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113 </param>
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114 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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115
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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116 <xml name="l1_ratio" token_default_value="0.15" token_help=" ">
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117 <param argument="l1_ratio" type="float" value="@DEFAULT_VALUE@" label="Elastic Net mixing parameter" help="@HELP@"/>
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118 </xml>
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119
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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120 <xml name="epsilon" token_default_value="0.1" token_help="Used if loss is ‘huber’, ‘epsilon_insensitive’, or ‘squared_epsilon_insensitive’. ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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121 <param argument="epsilon" type="float" value="@DEFAULT_VALUE@" label="Epsilon (epsilon-sensitive loss functions only)" help="@HELP@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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122 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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123
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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124 <xml name="learning_rate_s" token_help=" " token_selected1="false" token_selected2="false">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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125 <param argument="learning_rate" type="select" optional="true" label="Learning rate schedule" help="@HELP@">
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126 <option value="optimal" selected="@SELECTED1@">optimal</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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127 <option value="constant">constant</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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128 <option value="invscaling" selected="@SELECTED2@">inverse scaling</option>
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129 <yield/>
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130 </param>
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131 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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132
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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133 <xml name="eta0" token_default_value="0.0" token_help="Used with ‘constant’ or ‘invscaling’ schedules. ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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134 <param argument="eta0" type="float" value="@DEFAULT_VALUE@" label="Initial learning rate" help="@HELP@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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135 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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136
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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137 <xml name="power_t" token_default_value="0.5" token_help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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138 <param argument="power_t" type="float" value="@DEFAULT_VALUE@" label="Exponent for inverse scaling learning rate" help="@HELP@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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139 </xml>
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140
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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141 <xml name="normalize" token_checked="false" token_help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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142 <param argument="normalize" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="Normalize samples before training" help=" "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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143 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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144
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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145 <xml name="copy_X" token_checked="true" token_help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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146 <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. "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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147 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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148
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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149 <xml name="ridge_params">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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150 <expand macro="normalize"/>
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151 <expand macro="alpha" default_value="1.0"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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152 <expand macro="fit_intercept"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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153 <expand macro="max_iter" default_value=""/>
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154 <expand macro="tol" default_value="0.001" help_text="Precision of the solution. "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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155 <!--class_weight-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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156 <expand macro="copy_X"/>
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157 <param argument="solver" type="select" value="" label="Solver to use in the computational routines" help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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158 <option value="auto" selected="true">auto</option>
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159 <option value="svd">svd</option>
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160 <option value="cholesky">cholesky</option>
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161 <option value="lsqr">lsqr</option>
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162 <option value="sparse_cg">sparse_cg</option>
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163 <option value="sag">sag</option>
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164 </param>
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165 <expand macro="random_state"/>
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166 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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167
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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168 <!--Ensemble methods-->
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169 <xml name="n_estimators" token_default_value="10" token_help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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170 <param argument="n_estimators" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of trees in the forest" help="@HELP@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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171 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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172
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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173 <xml name="max_depth" token_default_value="" token_help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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174 <param argument="max_depth" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Maximum depth of the tree" help="@HELP@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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175 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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176
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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177 <xml name="min_samples_split" token_default_value="2" token_help=" ">
1
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178 <param argument="min_samples_split" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples required to split an internal node" help="@HELP@"/>
0
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179 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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180
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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181 <xml name="min_samples_leaf" token_default_value="1" token_help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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182 <param argument="min_samples_leaf" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Minimum number of samples in newly created leaves" help="@HELP@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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183 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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184
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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185 <xml name="min_weight_fraction_leaf" token_default_value="0.0" token_help=" ">
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186 <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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187 </xml>
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188
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189 <xml name="max_leaf_nodes" token_default_value="" token_help=" ">
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190 <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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191 </xml>
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192
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193 <xml name="bootstrap" token_checked="true" token_help=" ">
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194 <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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195 </xml>
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196
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197 <xml name="criterion" token_help=" ">
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198 <param argument="criterion" type="select" label="Function to measure the quality of a split" help=" ">
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199 <option value="gini" selected="true">Gini impurity</option>
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200 <option value="entropy">Information gain</option>
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201 <yield/>
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202 </param>
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203 </xml>
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204
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205 <xml name="oob_score" token_checked="false" token_help=" ">
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206 <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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207 </xml>
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208
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209 <xml name="max_features" token_default_value="auto" token_help="This could be an integer, float, string, or None. For more information please refer to help. ">
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210 <param argument="max_features" type="text" optional="true" value="@DEFAULT_VALUE@" label="Number of features for finding the best split" help="@HELP@"/>
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211 </xml>
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212
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213 <xml name="learning_rate" token_default_value="1.0" token_help=" ">
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214 <param argument="learning_rate" type="float" optional="true" value="@DEFAULT_VALUE@" label="Learning rate" help="@HELP@"/>
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215 </xml>
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216
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217
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218 <!--Parameters-->
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219 <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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220 <param argument="tol" type="float" optional="true" value="@DEFAULT_VALUE@" label="Tolerance" help="@HELP_TEXT@"/>
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221 </xml>
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222
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223 <xml name="n_clusters" token_default_value="8">
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224 <param argument="n_clusters" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of clusters" help=" "/>
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225 </xml>
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226
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227 <xml name="fit_intercept" token_checked="true">
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228 <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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229 </xml>
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230
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231 <xml name="n_iter" token_default_value="5" token_help_text="The number of passes over the training data (aka epochs). ">
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232 <param argument="n_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of iterations" help="@HELP_TEXT@"/>
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233 </xml>
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234
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235 <xml name="shuffle" token_checked="true" token_help_text=" " token_label="Shuffle data after each iteration">
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236 <param argument="shuffle" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="@CHECKED@" label="@LABEL@" help="@HELP_TEXT@"/>
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237 </xml>
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238
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239 <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.">
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240 <param argument="random_state" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Random seed number" help="@HELP_TEXT@"/>
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241 </xml>
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242
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243 <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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244 <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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245 </xml>
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246
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247 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term.">
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248 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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249 </xml>
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250
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251 <!--xml name="class_weight" token_default_value="" token_help_text="">
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252 <param argument="class_weight" type="" optional="true" value="@DEFAULT_VALUE@" label="" help="@HELP_TEXT@"/>
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253 </xml-->
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254
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255 <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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256 <param argument="alpha" type="float" optional="true" value="@DEFAULT_VALUE@" label="Regularization coefficient" help="@HELP_TEXT@"/>
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257 </xml>
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258
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259 <xml name="n_samples" token_default_value="100" token_help_text="The total number of points equally divided among clusters.">
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260 <param argument="n_samples" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of samples" help="@HELP_TEXT@"/>
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261 </xml>
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262
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263 <xml name="n_features" token_default_value="2" token_help_text="Number of different numerical properties produced for each sample.">
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264 <param argument="n_features" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of features" help="@HELP_TEXT@"/>
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265 </xml>
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266
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267 <xml name="noise" token_default_value="0.0" token_help_text="Floating point number. ">
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268 <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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269 </xml>
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270
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271 <xml name="C" token_default_value="1.0" token_help_text="Penalty parameter C of the error term. ">
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272 <param argument="C" type="float" optional="true" value="@DEFAULT_VALUE@" label="Penalty parameter" help="@HELP_TEXT@"/>
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273 </xml>
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274
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275 <xml name="max_iter" token_default_value="300" token_label="Maximum number of iterations per single run" token_help_text=" ">
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276 <param argument="max_iter" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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277 </xml>
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278
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279 <xml name="n_init" token_default_value="10" >
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280 <param argument="n_init" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Number of runs with different centroid seeds" help=" "/>
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281 </xml>
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282
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283 <xml name="init">
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284 <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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285 <option value="k-means++">k-means++</option>
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286 <option value="random">random</option>
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287 </param>
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288 </xml>
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289
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290 <xml name="gamma" token_default_value="1.0" token_label="Scaling parameter" token_help_text=" ">
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291 <param argument="gamma" type="float" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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292 </xml>
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293
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294 <xml name="degree" token_default_value="3" token_label="Degree of the polynomial" token_help_text=" ">
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295 <param argument="degree" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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296 </xml>
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297
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298 <xml name="coef0" token_default_value="1" token_label="Zero coefficient" token_help_text=" ">
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299 <param argument="coef0" type="integer" optional="true" value="@DEFAULT_VALUE@" label="@LABEL@" help="@HELP_TEXT@"/>
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300 </xml>
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301
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302 <xml name="pos_label" token_default_value="">
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303 <param argument="pos_label" type="integer" optional="true" value="@DEFAULT_VALUE@" label="Label of the positive class" help=" "/>
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304 </xml>
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305
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306 <xml name="average">
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307 <param argument="average" type="select" optional="true" label="Averaging type" help=" ">
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308 <option value="micro">Calculate metrics globally by counting the total true positives, false negatives and false positives. (micro)</option>
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309 <option value="samples">Calculate metrics for each instance, and find their average. Only meaningful for multilabel. (samples)</option>
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310 <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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311 <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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312 <option value="None">None</option>
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313 <yield/>
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314 </param>
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315 </xml>
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316
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317 <xml name="beta">
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318 <param argument="beta" type="float" value="1.0" label="The strength of recall versus precision in the F-score" help=" "/>
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319 </xml>
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320
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321
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322 <!--Data interface-->
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323 <xml name="tabular_input">
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324 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
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325 <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
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326 <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
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327 </xml>
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328
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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329 <xml name="sample_cols" token_label1="File containing true class labels:" token_label2="File containing predicted class labels:" token_multiple1="False" token_multiple2="False" token_format1="tabular" token_format2="tabular" token_help1="" token_help2="">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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330 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
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331 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
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332 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
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333 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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334 <yield/>
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335 </xml>
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336
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337 <xml name="samples_tabular" token_multiple1="False" token_multiple2="False">
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338 <param name="infile1" type="data" format="tabular" label="Training samples dataset:"/>
4
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339 <param name="header1" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
0
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340 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select target column(s):"/>
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341 <param name="infile2" type="data" format="tabular" label="Dataset containing class labels:"/>
4
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342 <param name="header2" type="boolean" optional="True" truevalue="booltrue" falsevalue="boolfalse" checked="False" label="Does the dataset contain header:" />
0
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343 <param name="col2" multiple="@MULTIPLE2@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
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344 <yield/>
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345 </xml>
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346
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347 <xml name="clf_inputs_extended" token_label1=" " token_label2=" " token_multiple="False">
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348 <conditional name="true_columns">
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349 <param name="selected_input1" type="select" label="Select the input type of true labels dataset:">
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350 <option value="tabular" selected="true">Tabular</option>
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351 <option value="sparse">Sparse</option>
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352 </param>
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353 <when value="tabular">
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354 <param name="infile1" type="data" label="@LABEL1@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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355 <param name="col1" type="data_column" data_ref="infile1" label="Select the target column:"/>
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356 </when>
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357 <when value="sparse">
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358 <param name="infile1" type="data" format="txt" label="@LABEL1@"/>
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359 </when>
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360 </conditional>
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361 <conditional name="predicted_columns">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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362 <param name="selected_input2" type="select" label="Select the input type of predicted labels dataset:">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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363 <option value="tabular" selected="true">Tabular</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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364 <option value="sparse">Sparse</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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365 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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366 <when value="tabular">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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367 <param name="infile2" type="data" label="@LABEL2@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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368 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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369 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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370 <when value="sparse">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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371 <param name="infile2" type="data" format="txt" label="@LABEL1@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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372 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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373 </conditional>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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374 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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375
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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376 <xml name="clf_inputs" token_label1="Dataset containing true labels (tabular):" token_label2="Dataset containing predicted values (tabular):" token_multiple1="False" token_multiple="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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377 <param name="infile1" type="data" format="tabular" label="@LABEL1@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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378 <param name="col1" multiple="@MULTIPLE1@" type="data_column" data_ref="infile1" label="Select the target column:"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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379 <param name="infile2" type="data" format="tabular" label="@LABEL2@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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380 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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381 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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382
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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383 <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.">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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384 <repeat name="@NAME@" min="1" max="@MAX_NUM@" title="Select input file(s):">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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385 <param name="input" type="data" format="@FORMAT@" label="@LABEL@" help="@HELP_TEXT@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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386 </repeat>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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387 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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388
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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389 <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="">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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390 <param name="infile1" type="data" format="@FORMAT1@" label="@LABEL1@" help="@HELP1@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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391 <param name="infile2" type="data" format="@FORMAT2@" label="@LABEL2@" help="@HELP2@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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392 <param name="col2" multiple="@MULTIPLE@" type="data_column" data_ref="infile2" label="Select target column(s):"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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393 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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394
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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395 <xml name="sl_mixed_input">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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396 <conditional name="input_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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397 <param name="selected_input" type="select" label="Select input type:">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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398 <option value="tabular" selected="true">tabular data</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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399 <option value="sparse">sparse matrix</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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400 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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401 <when value="tabular">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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402 <expand macro="samples_tabular" multiple1="true"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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403 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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404 <when value="sparse">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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405 <expand macro="sparse_target"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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406 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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407 </conditional>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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408 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
409
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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410 <xml name="multitype_input" token_format="tabular" token_help="All datasets with tabular format are supporetd.">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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411 <param name="infile_transform" type="data" format="@FORMAT@" label="Select a dataset to transform:" help="@HELP@"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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412 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
413
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
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414
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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415 <!--Advanced options-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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416 <xml name="nn_advanced_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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417 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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418 <yield/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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419 <param argument="weights" type="select" label="Weight function" help="Used in prediction.">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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420 <option value="uniform" selected="true">Uniform weights. All points in each neighborhood are weighted equally. (Uniform)</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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421 <option value="distance">Weight points by the inverse of their distance. (Distance)</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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422 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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423 <param argument="algorithm" type="select" label="Neighbor selection algorithm" help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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424 <option value="auto" selected="true">Auto</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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425 <option value="ball_tree">BallTree</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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426 <option value="kd_tree">KDTree</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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427 <option value="brute">Brute-force</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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428 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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429 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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430 <!--param name="metric"-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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431 <!--param name="p"-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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432 <!--param name="metric_params"-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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433 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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434 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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435
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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436 <xml name="svc_advanced_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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437 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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438 <yield/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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439 <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.">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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440 <option value="rbf" selected="true">rbf</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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441 <option value="linear">linear</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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442 <option value="poly">poly</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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443 <option value="sigmoid">sigmoid</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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444 <option value="precomputed">precomputed</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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445 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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446 <param argument="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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447 <!--TODO: param argument="gamma" float, optional (default=’auto’) -->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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448 <param argument="coef0" type="float" optional="true" value="0.0" label="Zero coefficient (polynomial and sigmoid kernels only)"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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449 help="Independent term in kernel function. dafault: 0.0 "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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450 <param argument="shrinking" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
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451 label="Use the shrinking heuristic" help=" "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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452 <param argument="probability" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
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453 label="Enable probability estimates. " help="This must be enabled prior to calling fit, and will slow down that method."/>
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454 <!-- param argument="cache_size"-->
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455 <!--expand macro="class_weight"/-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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456 <expand macro="tol" default_value="0.001" help_text="Tolerance for stopping criterion. "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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457 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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458 <!--param argument="decision_function_shape"-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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459 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
460 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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461 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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462
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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463 <xml name="spectral_clustering_advanced_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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464 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
465 <expand macro="n_clusters"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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466 <param argument="eigen_solver" type="select" value="" label="Eigen solver" help="The eigenvalue decomposition strategy to use.">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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467 <option value="arpack" selected="true">arpack</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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468 <option value="lobpcg">lobpcg</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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469 <option value="amg">amg</option>
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470 <!--None-->
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471 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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472 <expand macro="random_state"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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473 <expand macro="n_init"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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474 <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''."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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475 <param argument="affinity" type="select" label="Affinity" help="Affinity kernel to use. ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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476 <option value="rbf" selected="true">RBF</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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477 <option value="precomputed">precomputed</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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478 <option value="nearest_neighbors">Nearset neighbors</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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479 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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480 <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''"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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481 <!--param argument="eigen_tol"-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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482 <param argument="assign_labels" type="select" label="Assign labels" help="The strategy to use to assign labels in the embedding space.">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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483 <option value="kmeans" selected="true">kmeans</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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484 <option value="discretize">discretize</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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485 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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486 <param argument="degree" type="integer" optional="true" value="3"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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487 label="Degree of the polynomial (polynomial kernel only)" help="Ignored by other kernels. dafault : 3 "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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488 <param argument="coef0" type="integer" optional="true" value="1"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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489 label="Zero coefficient (polynomial and sigmoid kernels only)" help="Ignored by other kernels. dafault : 1 "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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490 <!--param argument="kernel_params"-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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491 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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492 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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493
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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494 <xml name="minibatch_kmeans_advanced_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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495 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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496 <expand macro="n_clusters"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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497 <expand macro="init"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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498 <expand macro="n_init" default_value="3"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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499 <expand macro="max_iter" default_value="100"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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500 <expand macro="tol" help_text="Early stopping heuristics based on normalized center change. To disable set to 0.0 ."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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501 <expand macro="random_state"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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502 <param argument="batch_size" type="integer" optional="true" value="100" label="Batch size" help="Size of the mini batches."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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503 <!--param argument="compute_labels"-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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504 <param argument="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts" help="
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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505 Convergence detection based on inertia (the consecutive number of mini batches that doe not yield an improvement on the smoothed inertia).
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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506 To disable, set max_no_improvement to None. "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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507 <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 )"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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508 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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509 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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510 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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511
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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512 <xml name="kmeans_advanced_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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513 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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514 <expand macro="n_clusters"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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515 <expand macro="init"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
516 <expand macro="n_init"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
517 <expand macro="max_iter"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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518 <expand macro="tol" default_value="0.0001" help_text="Relative tolerance with regards to inertia to declare convergence."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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519 <!--param argument="precompute_distances"/-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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520 <expand macro="random_state"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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521 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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522 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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523 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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524
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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525 <xml name="birch_advanced_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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526 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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527 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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528 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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529 <expand macro="n_clusters" default_value="3"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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530 <!--param argument="compute_labels"/-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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531 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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532 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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533
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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534 <xml name="dbscan_advanced_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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535 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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536 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
537 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
538 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
539 <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.">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
540 <option value="auto" selected="true">auto</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
541 <option value="ball_tree">ball_tree</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
542 <option value="kd_tree">kd_tree</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
543 <option value="brute">brute</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
544 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
545 <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."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
546 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
547 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
548
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
549 <xml name="clustering_algorithms_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
550 <conditional name="algorithm_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
551 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
552 <option value="KMeans" selected="true">KMeans</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
553 <option value="SpectralClustering">Spectral Clustering</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
554 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
555 <option value="DBSCAN">DBSCAN</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
556 <option value="Birch">Birch</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
557 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
558 <when value="KMeans">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
559 <expand macro="kmeans_advanced_options"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
560 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
561 <when value="DBSCAN">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
562 <expand macro="dbscan_advanced_options"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
563 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
564 <when value="Birch">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
565 <expand macro="birch_advanced_options"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
566 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
567 <when value="SpectralClustering">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
568 <expand macro="spectral_clustering_advanced_options"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
569 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
570 <when value="MiniBatchKMeans">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
571 <expand macro="minibatch_kmeans_advanced_options"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
572 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
573 </conditional>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
574 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
575
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
576 <xml name="distance_metrics">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
577 <param argument="metric" type="select" label="Distance metric" help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
578 <option value="euclidean" selected="true">euclidean</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
579 <option value="cityblock">cityblock</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
580 <option value="cosine">cosine</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
581 <option value="l1">l1</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
582 <option value="l2">l2</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
583 <option value="manhattan">manhattan</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
584 <yield/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
585 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
586 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
587
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
588 <xml name="distance_nonsparse_metrics">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
589 <option value="braycurtis">braycurtis</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
590 <option value="canberra">canberra</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
591 <option value="chebyshev">chebyshev</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
592 <option value="correlation">correlation</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
593 <option value="dice">dice</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
594 <option value="hamming">hamming</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
595 <option value="jaccard">jaccard</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
596 <option value="kulsinski">kulsinski</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
597 <option value="mahalanobis">mahalanobis</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
598 <option value="matching">matching</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
599 <option value="minkowski">minkowski</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
600 <option value="rogerstanimoto">rogerstanimoto</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
601 <option value="russellrao">russellrao</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
602 <option value="seuclidean">seuclidean</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
603 <option value="sokalmichener">sokalmichener</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
604 <option value="sokalsneath">sokalsneath</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
605 <option value="sqeuclidean">sqeuclidean</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
606 <option value="yule">yule</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
607 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
608
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
609 <xml name="pairwise_kernel_metrics">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
610 <param argument="metric" type="select" label="Pirwise Kernel metric" help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
611 <option value="rbf" selected="true">rbf</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
612 <option value="sigmoid">sigmoid</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
613 <option value="polynomial">polynomial</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
614 <option value="linear" selected="true">linear</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
615 <option value="chi2">chi2</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
616 <option value="additive_chi2">additive_chi2</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
617 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
618 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
619
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
620 <xml name="sparse_pairwise_metric_functions">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
621 <param name="selected_metric_function" type="select" label="Select the pairwise metric you want to compute:">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
622 <option value="euclidean_distances" selected="true">Euclidean distance matrix</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
623 <option value="pairwise_distances">Distance matrix</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
624 <option value="pairwise_distances_argmin">Minimum distances between one point and a set of points</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
625 <yield/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
626 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
627 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
628
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
629 <xml name="pairwise_metric_functions">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
630 <option value="additive_chi2_kernel" >Additive chi-squared kernel</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
631 <option value="chi2_kernel">Exponential chi-squared kernel</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
632 <option value="linear_kernel">Linear kernel</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
633 <option value="manhattan_distances">L1 distances</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
634 <option value="pairwise_kernels">Kernel</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
635 <option value="polynomial_kernel">Polynomial kernel</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
636 <option value="rbf_kernel">Gaussian (rbf) kernel</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
637 <option value="laplacian_kernel">Laplacian kernel</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
638 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
639
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
640 <xml name="sparse_pairwise_condition">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
641 <when value="pairwise_distances">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
642 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
643 <expand macro="distance_metrics">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
644 <yield/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
645 </expand>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
646 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
647 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
648 <when value="euclidean_distances">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
649 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
650 <param argument="squared" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="false"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
651 label="Return squared Euclidean distances" help=" "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
652 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
653 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
654 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
655
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
656 <xml name="argmin_distance_condition">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
657 <when value="pairwise_distances_argmin">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
658 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
659 <param argument="axis" type="integer" optional="true" value="1" label="Axis" help="Axis along which the argmin and distances are to be computed."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
660 <expand macro="distance_metrics">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
661 <yield/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
662 </expand>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
663 <param argument="batch_size" type="integer" optional="true" value="500" label="Batch size" help="Number of rows to be processed in each batch run."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
664 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
665 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
666 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
667
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
668 <xml name="sparse_preprocessors">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
669 <param name="selected_pre_processor" type="select" label="Select a preprocessor:">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
670 <option value="StandardScaler" selected="true">Standard Scaler (Standardizes features by removing the mean and scaling to unit variance)</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
671 <option value="Binarizer">Binarizer (Binarizes data)</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
672 <option value="Imputer">Imputer (Completes missing values)</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
673 <option value="MaxAbsScaler">Max Abs Scaler (Scales features by their maximum absolute value)</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
674 <option value="Normalizer">Normalizer (Normalizes samples individually to unit norm)</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
675 <yield/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
676 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
677 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
678
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
679 <xml name="sparse_preprocessor_options">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
680 <when value="Binarizer">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
681 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
682 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
683 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
684 label="Use a copy of data for precomputing binarization" help=" "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
685 <param argument="threshold" type="float" optional="true" value="0.0"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
686 label="Threshold"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
687 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. "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
688 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
689 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
690 <when value="Imputer">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
691 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
692 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
693 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
694 label="Use a copy of data for precomputing imputation" help=" "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
695 <param argument="strategy" type="select" optional="true" label="Imputation strategy" help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
696 <option value="mean" selected="true">Replace missing values using the mean along the axis</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
697 <option value="median">Replace missing values using the median along the axis</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
698 <option value="most_frequent">Replace missing using the most frequent value along the axis</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
699 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
700 <param argument="missing_values" type="text" optional="true" value="NaN"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
701 label="Placeholder for missing values" help="For missing values encoded as numpy.nan, use the string value “NaN”"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
702 <param argument="axis" type="boolean" optional="true" truevalue="1" falsevalue="0"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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parents:
diff changeset
703 label="Impute along axis = 1" help="If fasle, axis = 0 is selected for imputation. "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
704 <!--param argument="axis" type="select" optional="true" label="The axis along which to impute" help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
705 <option value="0" selected="true">Impute along columns</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
706 <option value="1">Impute along rows</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
707 </param-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
708 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
709 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
710 <when value="StandardScaler">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
711 <expand macro="multitype_input"/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
712 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
713 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
714 label="Use a copy of data for performing inplace scaling" help=" "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
715 <param argument="with_mean" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
716 label="Center the data before scaling" help=" "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
717 <param argument="with_std" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
718 label="Scale the data to unit variance (or unit standard deviation)" help=" "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
719 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
720 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
721 <when value="MaxAbsScaler">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
722 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
723 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
724 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
725 label="Use a copy of data for precomputing scaling" help=" "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
726 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
727 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
728 <when value="Normalizer">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
729 <expand macro="multitype_input" format="tabular,txt" help="Tabular and sparse datasets are supporetd."/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
730 <section name="options" title="Advanced Options" expanded="False">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
731 <param argument="norm" type="select" optional="true" label="The norm to use to normalize non zero samples" help=" ">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
732 <option value="l1" selected="true">l1</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
733 <option value="l2">l2</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
734 <option value="max">max</option>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
735 </param>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
736 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="true"
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
737 label="Use a copy of data for precomputing row normalization" help=" "/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
738 </section>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
739 </when>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
740 <yield/>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
741 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
742
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
743 <!-- Outputs -->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
744
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
745 <xml name="output">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
746 <outputs>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
747 <data format="tabular" name="outfile_predict">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
748 <filter>selected_tasks['selected_task'] == 'load'</filter>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
749 </data>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
750 <data format="zip" name="outfile_fit">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
751 <filter>selected_tasks['selected_task'] == 'train'</filter>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
752 </data>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
753 </outputs>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
754 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
755
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
756
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
757 <!--Citations-->
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
758 <xml name="eden_citation">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
759 <citations>
3
bf0ea4cece8b planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 99231ce3ef238975a6614926f2fa6326b9454ee8
bgruening
parents: 2
diff changeset
760 <citation type="doi">10.5281/zenodo.15094</citation>
0
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
761 </citations>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
762 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
763
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
764 <xml name="sklearn_citation">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
765 <citations>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
766 <citation type="bibtex">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
767 @article{scikit-learn,
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
768 title={Scikit-learn: Machine Learning in {P}ython},
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
769 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
770 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
771 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
772 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
773 journal={Journal of Machine Learning Research},
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
774 volume={12},
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
775 pages={2825--2830},
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
776 year={2011}
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
777 url = {https://github.com/scikit-learn/scikit-learn}
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
778 }
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
779 </citation>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
780 </citations>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
781 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
782
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
783 <xml name="scipy_citation">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
784 <citations>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
785 <citation type="bibtex">
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
786 @Misc{,
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
787 author = {Eric Jones and Travis Oliphant and Pearu Peterson and others},
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
788 title = {{SciPy}: Open source scientific tools for {Python}},
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
789 year = {2001--},
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
790 url = "http://www.scipy.org/",
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
791 note = {[Online; accessed 2016-04-09]}
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
792 }
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
793 </citation>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
794 </citations>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
795 </xml>
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
796
dec5e182fd0c planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
797 </macros>