Mercurial > repos > bgruening > sklearn_numeric_clustering

annotate numeric_clustering.xml @ 8:85d31935d4a2 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 79fe42239dcf077b13f85cbcd6c6e30d7e1e4832
author bgruening
date Tue, 22 May 2018 19:31:34 -0400
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children 40f3318b61c2
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c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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1 <tool id="sklearn_numeric_clustering" name="Numeric Clustering" version="@VERSION@">
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2 <description></description>
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3 <macros>
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4 <import>main_macros.xml</import>
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5 </macros>
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6 <expand macro="python_requirements"/>
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7 <expand macro="macro_stdio"/>
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8 <version_command>echo "@VERSION@"</version_command>
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9 <command><![CDATA[
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10 python "$cluster_script" '$inputs'
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11 ]]>
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12 </command>
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13 <configfiles>
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14 <inputs name="inputs"/>
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15 <configfile name="cluster_script">
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16 <![CDATA[
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17 import sys
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18 import json
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19 import numpy as np
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20 import sklearn.cluster
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21 import pandas
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22 from sklearn import metrics
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23 from scipy.io import mmread
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25 input_json_path = sys.argv[1]
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26 params = json.load(open(input_json_path, "r"))
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27
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28 selected_algorithm = params["input_types"]["algorithm_options"]["selected_algorithm"]
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29
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30 my_class = getattr(sklearn.cluster, selected_algorithm)
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31 cluster_object = my_class()
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32 options = params["input_types"]["algorithm_options"]["options"]
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33
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34 cluster_object.set_params(**options)
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35
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36 #if $input_types.selected_input_type == "sparse":
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37 data_matrix = mmread(open("$infile", 'r'))
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38 #else:
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39 data = pandas.read_csv("$infile", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False )
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40
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41 start_column = $input_types.start_column
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42 end_column = $input_types.end_column
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43
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44 if end_column and start_column:
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45 if end_column >= start_column:
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46 data_matrix = data.values[:, start_column-1:end_column]
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47 else:
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48 data_matrix = data.values
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49 else:
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50 data_matrix = data.values
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51 #end if
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52
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53 prediction = cluster_object.fit_predict( data_matrix )
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54
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55 if len(np.unique(prediction)) > 1:
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56 silhouette_score = metrics.silhouette_score(data_matrix,prediction,metric='euclidean')
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57 else:
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58 silhouette_score = -1
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59 sys.stdout.write('silhouette score:' + '\t' + str(silhouette_score) + '\n')
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60
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61 prediction_df = pandas.DataFrame(prediction)
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62
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63 #if $input_types.selected_input_type == "sparse":
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64 res = prediction_df
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65 #else:
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66 res = pandas.concat([data, prediction_df], axis=1)
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67 #end if
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68
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69 res.to_csv(path_or_buf = "$outfile", sep="\t", index=False, header=False)
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70 ]]>
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71 </configfile>
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72 </configfiles>
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73 <inputs>
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74 <conditional name="input_types">
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75 <param name="selected_input_type" type="select" label="Select the format of input data">
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76 <option value="tabular" selected="true">Tabular Format (tabular, txt)</option>
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77 <option value="sparse">Sparse Vector Representation (mtx)</option>
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78 </param>
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79 <when value="sparse">
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80 <param name="infile" type="data" format="txt" label="Sparse vector (scipy.sparse.csr_matrix) file:" help="The following clustering algorithms support sparse matrix operations: ''Birch'', ''DBSCAN'', ''KMeans'', ''Mini BatchK Means'', and ''Spectral Clustering''. If your data is in tabular format, please use other clustering algorithms."/>
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81 <expand macro="clustering_algorithms_options"/>
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82 </when>
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83 <when value="tabular">
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84 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
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85 <param name="start_column" type="data_column" data_ref="infile" optional="True" label="Select a subset of data. Start column:" />
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86 <param name="end_column" type="data_column" data_ref="infile" optional="True" label="End column:" />
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87 <!--expand macro="clustering_algorithms_options"-->
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88 <conditional name="algorithm_options">
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89 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
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90 <option value="AgglomerativeClustering">Hierarchical Agglomerative Clustering</option>
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91 <option value="AffinityPropagation">Affinity Propagation</option>
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92 <option value="SpectralClustering">Spectral Clustering</option>
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93 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
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94 <option value="MeanShift">MeanShift</option>
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95 <option value="KMeans">KMeans</option>
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96 <option value="DBSCAN">DBSCAN</option>
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97 <option value="Birch">Birch</option>
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98 </param>
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99 <when value="KMeans">
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100 <expand macro="kmeans_advanced_options"/>
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101 </when>
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102 <when value="DBSCAN">
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103 <expand macro="dbscan_advanced_options"/>
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104 </when>
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105 <when value="Birch">
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106 <expand macro="birch_advanced_options"/>
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107 </when>
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108 <when value="SpectralClustering">
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109 <expand macro="spectral_clustering_advanced_options"/>
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110 </when>
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111 <when value="MiniBatchKMeans">
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112 <expand macro="minibatch_kmeans_advanced_options"/>
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113 </when>
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114 <when value="AffinityPropagation">
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115 <section name="options" title="Advanced Options" expanded="False">
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116 <param argument="damping" type="float" optional="true" value="0.5" label="Damping factor" help="Damping factor between 0.5 and 1."/>
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117 <expand macro="max_iter" default_value="200"/>
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118 <param argument="convergence_iter" type="integer" optional="true" value="15" label="Number of iterations at each convergence step" help="Number of iterations with no change in the number of estimated clusters that stops the convergence."/>
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119 <param argument="copy" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Copy" help="If False, the affinity matrix is modified inplace by the algorithm, for memory efficiency."/>
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120 <!--param argument="preference"/-->
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121 <param argument="affinity" type="select" label="Affinity" help="Affinity to use; euclidean uses the negative squared euclidean distance between points.">
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122 <option value="euclidean">Euclidean</option>
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123 <option value="precomputed">precomputed</option>
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124 </param>
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125 </section>
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126 </when>
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127 <when value="MeanShift">
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128 <section name="options" title="Advanced Options" expanded="False">
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129 <param argument="bandwidth" type="float" optional="true" value="" label="Kernel bandwidth" help="Bandwidth used in the RBF kernel. If not given, it will be computed using a heuristic based on the median of all pairwise distances."/>
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130 <!--param argument="seeds"/-->
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131 <param argument="bin_seeding" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Discretize initial kernel locations" help="If true, initial kernel locations are the bins grid whose coarseness corresponds to the bandwidth, speeding up the algorithm."/>
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132 <param argument="min_bin_freq" type="integer" optional="true" value="1" label="Minimum number of seeds per bin" help="To speed up the algorithm, accept only those bins with at least min_bin_freq points as seeds."/>
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133 <param argument="cluster_all" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolflase" checked="true" label="Cluster all" help="If true, all points (including orphans) are clustered. If false, orphans are given cluster label -1."/>
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134 </section>
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135 </when>
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136 <when value="AgglomerativeClustering">
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137 <section name="options" title="Advanced Options" expanded="False">
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138 <expand macro="n_clusters" default_value="2" />
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139 <param argument="affinity" type="select" label="Affinity" help="Metric used to compute the linkage. If linkage is ''ward'', only ''euclidean'' is accepted.">
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140 <option value="euclidean">Euclidean</option>
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141 <option value="manhattan">Manhattan</option>
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142 <option value="l1">L1</option>
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143 <option value="l2">L2</option>
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144 <option value="cosine">cosine</option>
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145 <option value="precomputed">precomputed</option>
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146 </param>
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147 <!--param argument="memory"-->
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148 <!--param argument="connectivity"-->
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149 <!--param argument="n_components"/-->
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150 <!--param argument="compute_full_tree"-->
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151 <param argument="linkage" type="select" optional="true" label="Linkage" help="">
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152 <option value="ward" selected="true">ward</option>
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153 <option value="complete">complete</option>
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154 <option value="average">average</option>
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155 </param>
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156 <!--param argument="pooling_func"-->
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157 </section>
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158 </when>
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159 </conditional>
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160 </when>
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161 </conditional>
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162 </inputs>
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163 <outputs>
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164 <data format="tabular" name="outfile"/>
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165 </outputs>
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166 <tests>
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167 <test>
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168 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
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169 <param name="selected_input_type" value="tabular"/>
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170 <param name="selected_algorithm" value="KMeans"/>
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171 <param name="start_column" value="2" />
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172 <param name="end_column" value="4" />
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173 <param name="n_clusters" value="4" />
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174 <param name="init" value="k-means++" />
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175 <param name="random_state" value="100"/>
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176 <output name="outfile" file="cluster_result01.txt"/>
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177 </test>
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178 <test>
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179 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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180 <param name="selected_algorithm" value="KMeans"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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181 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
182 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
183 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
184 <param name="n_clusters" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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185 <param name="init" value="random" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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186 <param name="random_state" value="100"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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187 <output name="outfile" file="cluster_result02.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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188 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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189 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
190 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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191 <param name="selected_algorithm" value="DBSCAN"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
192 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
193 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
194 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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195 <param name="algorithm" value="kd_tree"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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196 <param name="leaf_size" value="10"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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197 <param name="eps" value="1.0"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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198 <output name="outfile" file="cluster_result03.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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199 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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200 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
201 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
202 <param name="selected_algorithm" value="Birch"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
203 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
204 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
205 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
206 <param name="n_clusters" value="4"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
207 <param name="threshold" value="0.008"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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208 <output name="outfile" file="cluster_result04.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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209 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
210 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
211 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
212 <param name="selected_algorithm" value="Birch"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
213 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
214 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
215 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
216 <param name="branching_factor" value="20"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
217 <output name="outfile" file="cluster_result05.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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218 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
219 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
220 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
221 <param name="selected_algorithm" value="AffinityPropagation"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
222 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
223 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
224 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
225 <param name="affinity" value="euclidean"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
226 <param name="copy" value="false"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
227 <output name="outfile" file="cluster_result06.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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228 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
229 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
230 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
231 <param name="selected_algorithm" value="AffinityPropagation"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
232 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
233 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
234 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
235 <param name="damping" value="0.8"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
236 <output name="outfile" file="cluster_result07.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
237 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
238 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
239 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
240 <param name="selected_algorithm" value="MeanShift"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
241 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
242 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
243 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
244 <param name="min_bin_freq" value="3"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
245 <output name="outfile" file="cluster_result08.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
246 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
247 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
248 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
249 <param name="selected_algorithm" value="MeanShift"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
250 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
251 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
252 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
253 <param name="cluster_all" value="False"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
254 <output name="outfile" file="cluster_result09.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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255 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
256 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
257 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
258 <param name="selected_algorithm" value="AgglomerativeClustering"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
259 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
260 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
261 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
262 <param name="affinity" value="euclidean"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
263 <param name="linkage" value="average"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
264 <param name="n_clusters" value="4"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
265 <output name="outfile" file="cluster_result10.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
266 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
267 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
268 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
269 <param name="selected_algorithm" value="AgglomerativeClustering"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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270 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
271 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
272 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
273 <param name="linkage" value="complete"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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274 <param name="n_clusters" value="4"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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275 <output name="outfile" file="cluster_result11.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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276 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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277 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
278 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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279 <param name="selected_algorithm" value="SpectralClustering"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
280 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
281 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
282 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
283 <param name="eigen_solver" value="arpack"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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284 <param name="n_neighbors" value="12"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
285 <param name="n_clusters" value="4"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
286 <param name="assign_labels" value="discretize"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
287 <param name="random_state" value="100"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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288 <output name="outfile" file="cluster_result12" compare="sim_size" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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289 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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290 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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291 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
292 <param name="selected_algorithm" value="SpectralClustering"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
293 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
294 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
295 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
296 <param name="assign_labels" value="discretize"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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297 <param name="random_state" value="100"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
298 <param name="degree" value="2"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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299 <output name="outfile" file="cluster_result13.txt" compare="sim_size" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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300 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
301 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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302 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
303 <param name="selected_algorithm" value="MiniBatchKMeans"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
304 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
305 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
306 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
307 <param name="tol" value="0.5"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
308 <param name="random_state" value="100"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
309 <output name="outfile" file="cluster_result14.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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310 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
311 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
312 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
313 <param name="selected_algorithm" value="MiniBatchKMeans"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
314 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
315 <param name="n_init" value="5"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
316 <param name="start_column" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
317 <param name="end_column" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
318 <param name="batch_size" value="10"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
319 <param name="n_clusters" value="4"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
320 <param name="random_state" value="100"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
321 <param name="reassignment_ratio" value="1.0"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
322 <output name="outfile" file="cluster_result15.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
323 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
324 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
325 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
326 <param name="selected_algorithm" value="KMeans"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
327 <param name="selected_input_type" value="tabular"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
328 <param name="start_column" value="1" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
329 <param name="end_column" value="1" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
330 <param name="n_clusters" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
331 <param name="random_state" value="100"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
332 <output name="outfile" file="cluster_result16.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
333 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
334 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
335 <param name="infile" value="sparse.mtx" ftype="txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
336 <param name="selected_input_type" value="sparse"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
337 <param name="selected_algorithm" value="KMeans"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
338 <param name="n_clusters" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
339 <param name="init" value="k-means++" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
340 <param name="random_state" value="100"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
341 <output name="outfile" file="cluster_result17.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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342 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
343 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
344 <param name="infile" value="sparse.mtx" ftype="txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
345 <param name="selected_algorithm" value="DBSCAN"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
346 <param name="selected_input_type" value="sparse"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
347 <param name="algorithm" value="kd_tree"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
348 <param name="leaf_size" value="10"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
349 <param name="eps" value="1.0"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
350 <output name="outfile" file="cluster_result18.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
351 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
352 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
353 <param name="infile" value="sparse.mtx" ftype="txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
354 <param name="selected_algorithm" value="Birch"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
355 <param name="selected_input_type" value="sparse"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
356 <param name="n_clusters" value="2"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
357 <param name="threshold" value="0.008"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
358 <output name="outfile" file="cluster_result19.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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359 </test>
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360 <test>
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361 <param name="infile" value="sparse.mtx" ftype="txt"/>
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362 <param name="selected_algorithm" value="MiniBatchKMeans"/>
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363 <param name="selected_input_type" value="sparse"/>
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364 <param name="n_init" value="5"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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365 <param name="batch_size" value="10"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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366 <param name="n_clusters" value="2"/>
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367 <param name="random_state" value="100"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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368 <param name="reassignment_ratio" value="1.0"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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369 <output name="outfile" file="cluster_result20.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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370 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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371 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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372 <param name="infile" value="sparse.mtx" ftype="txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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373 <param name="selected_algorithm" value="SpectralClustering"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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374 <param name="selected_input_type" value="sparse"/>
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375 <param name="assign_labels" value="discretize"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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376 <param name="n_clusters" value="2"/>
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377 <param name="random_state" value="100"/>
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378 <param name="degree" value="2"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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379 <output name="outfile" file="cluster_result21.txt"/>
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380 </test>
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381 </tests>
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382 <help><![CDATA[
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383 **What it does**
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384 This tool offers different clustering algorithms which are provided by
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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385 scikit-learn to find similarities among samples and cluster the samples based on these similarities.
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386 ]]></help>
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387 <expand macro="sklearn_citation"/>
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388 </tool>