Mercurial > repos > bgruening > sklearn_numeric_clustering

annotate numeric_clustering.xml @ 45:838ca001438d draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5eca9041ce0154eded5aec07195502d5eb3cdd4f
author bgruening
date Fri, 03 Nov 2023 23:25:01 +0000
parents 06d772036a62
children
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06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
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1 <tool id="sklearn_numeric_clustering" name="Numeric Clustering" version="@VERSION@" profile="@PROFILE@">
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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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23 from sklearn import metrics
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24 from scipy.io import mmread
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25 from galaxy_ml.utils import read_columns
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28 N_JOBS = int(__import__('os').environ.get('GALAXY_SLOTS', 1))
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30 input_json_path = sys.argv[1]
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31 with open(input_json_path, "r") as param_handler:
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32 params = json.load(param_handler)
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35 selected_algorithm = params["input_types"]["algorithm_options"]["selected_algorithm"]
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37 my_class = getattr(sklearn.cluster, selected_algorithm)
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38 cluster_object = my_class()
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39 options = params["input_types"]["algorithm_options"]["options"]
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41 cluster_object.set_params(**options)
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42 if 'n_jobs' in cluster_object.get_params():
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43 cluster_object.set_params( n_jobs=N_JOBS )
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44
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45 header = None
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46 #if $input_types.selected_input_type == "sparse":
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47 data_matrix = mmread("$infile")
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48 #else:
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49 data = pandas.read_csv("$infile", sep='\t', header=header, index_col=None, parse_dates=True, encoding=None)
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50
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51 header = 'infer' if params["input_types"]["header"] else None
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52 column_option = params["input_types"]["column_selector_options"]["selected_column_selector_option"]
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53 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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54 c = params["input_types"]["column_selector_options"]["col"]
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55 else:
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56 c = None
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57 data_matrix = read_columns(
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58 "$infile",
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59 c = c,
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60 c_option = column_option,
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61 sep='\t',
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62 header=header,
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63 parse_dates=True,
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64 encoding=None)
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65 #end if
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67 prediction = cluster_object.fit_predict( data_matrix )
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68
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69 if len(np.unique(prediction)) > 1:
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70 silhouette_score = metrics.silhouette_score(data_matrix,prediction,metric='euclidean')
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71 else:
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72 silhouette_score = -1
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73 sys.stdout.write('silhouette score:' + '\t' + str(silhouette_score) + '\n')
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74
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75 prediction_df = pandas.DataFrame(prediction, columns=["predicted"])
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77 #if $input_types.selected_input_type == "sparse":
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78 res = prediction_df
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79 #else:
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80 res = pandas.concat([data, prediction_df], axis=1)
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81 #end if
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82
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83 res.to_csv(path_or_buf = "$outfile", sep="\t", index=False, header=False)
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84 ]]>
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85 </configfile>
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86 </configfiles>
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87 <inputs>
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88 <conditional name="input_types">
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89 <param name="selected_input_type" type="select" label="Select the format of input data">
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90 <option value="tabular" selected="true">Tabular Format (tabular, txt)</option>
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91 <option value="sparse">Sparse Vector Representation (mtx)</option>
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92 </param>
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93 <when value="sparse">
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94 <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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95 <expand macro="clustering_algorithms_options" />
0
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96 </when>
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97 <when value="tabular">
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98 <param name="infile" type="data" format="tabular" label="Data file with numeric values" />
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99 <param name="header" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="True" label="Does the dataset contain header:" />
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100 <conditional name="column_selector_options">
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101 <expand macro="samples_column_selector_options" col_name="col" multiple="true" infile="infile" />
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102 </conditional>
0
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103 <!--expand macro="clustering_algorithms_options"-->
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104 <conditional name="algorithm_options">
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105 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
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106 <option value="AgglomerativeClustering">Hierarchical Agglomerative Clustering</option>
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107 <option value="AffinityPropagation">Affinity Propagation</option>
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108 <option value="SpectralClustering">Spectral Clustering</option>
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109 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
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110 <option value="MeanShift">MeanShift</option>
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111 <option value="KMeans">KMeans</option>
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112 <option value="DBSCAN">DBSCAN</option>
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113 <option value="Birch">Birch</option>
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114 </param>
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115 <when value="KMeans">
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116 <expand macro="kmeans_advanced_options" />
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117 </when>
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118 <when value="DBSCAN">
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119 <expand macro="dbscan_advanced_options" />
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120 </when>
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121 <when value="Birch">
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122 <expand macro="birch_advanced_options" />
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123 </when>
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124 <when value="SpectralClustering">
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125 <expand macro="spectral_clustering_advanced_options" />
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126 </when>
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127 <when value="MiniBatchKMeans">
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128 <expand macro="minibatch_kmeans_advanced_options" />
0
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129 </when>
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130 <when value="AffinityPropagation">
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131 <section name="options" title="Advanced Options" expanded="False">
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132 <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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133 <expand macro="max_iter" default_value="200" />
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134 <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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135 <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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136 <!--param argument="preference"/-->
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137 <param argument="affinity" type="select" label="Affinity" help="Affinity to use; euclidean uses the negative squared euclidean distance between points.">
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138 <option value="euclidean">Euclidean</option>
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139 <option value="precomputed">precomputed</option>
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140 </param>
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141 </section>
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142 </when>
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143 <when value="MeanShift">
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144 <section name="options" title="Advanced Options" expanded="False">
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145 <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." />
0
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146 <!--param argument="seeds"/-->
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147 <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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148 <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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149 <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." />
0
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150 </section>
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151 </when>
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152 <when value="AgglomerativeClustering">
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153 <section name="options" title="Advanced Options" expanded="False">
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154 <expand macro="n_clusters" default_value="2" />
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155 <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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156 <option value="euclidean">Euclidean</option>
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157 <option value="manhattan">Manhattan</option>
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158 <option value="l1">L1</option>
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159 <option value="l2">L2</option>
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160 <option value="cosine">cosine</option>
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161 <option value="precomputed">precomputed</option>
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162 </param>
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163 <!--param argument="memory"-->
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164 <!--param argument="connectivity"-->
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165 <!--param argument="n_components"/-->
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166 <!--param argument="compute_full_tree"-->
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167 <param argument="linkage" type="select" optional="true" label="Linkage" help="">
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168 <option value="ward" selected="true">ward</option>
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169 <option value="complete">complete</option>
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170 <option value="average">average</option>
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171 <option value="single">single</option>
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172 </param>
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173 <!--param argument="pooling_func"-->
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174 </section>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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175 </when>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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176 </conditional>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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177 </when>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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178 </conditional>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
179 </inputs>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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180 <outputs>
34
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bgruening
parents: 31
diff changeset
181 <data format="tabular" name="outfile" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
182 </outputs>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
183 <tests>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
184 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
185 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
186 <param name="selected_input_type" value="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
187 <param name="selected_algorithm" value="KMeans" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 34
diff changeset
188 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
189 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
190 <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
191 <param name="init" value="k-means++" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
192 <param name="random_state" value="100" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
193 <output name="outfile" file="cluster_result01.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
194 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
195 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
196 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
197 <param name="selected_algorithm" value="KMeans" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
198 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 34
diff changeset
199 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
200 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
201 <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
202 <param name="init" value="random" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
203 <param name="random_state" value="100" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
204 <output name="outfile" file="cluster_result02.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
205 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
206 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
207 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
208 <param name="selected_algorithm" value="DBSCAN" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
209 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 34
diff changeset
210 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
211 <param name="col" value="2,3,4" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
212 <param name="algorithm" value="kd_tree" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
213 <param name="leaf_size" value="10" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
214 <param name="eps" value="1.0" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
215 <output name="outfile" file="cluster_result03.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
216 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
217 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
218 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
219 <param name="selected_algorithm" value="Birch" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
220 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 34
diff changeset
221 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
222 <param name="col" value="2,3,4" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
223 <param name="n_clusters" value="4" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
224 <param name="threshold" value="0.008" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
225 <output name="outfile" file="cluster_result04.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
226 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
227 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
228 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
229 <param name="selected_algorithm" value="Birch" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
230 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 34
diff changeset
231 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
232 <param name="col" value="2,3,4" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
233 <param name="branching_factor" value="20" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
234 <output name="outfile" file="cluster_result05.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
235 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
236 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
237 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
238 <param name="selected_algorithm" value="AffinityPropagation" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
239 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 34
diff changeset
240 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
241 <param name="col" value="2,3,4" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
242 <param name="affinity" value="euclidean" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
243 <param name="copy" value="false" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
244 <output name="outfile" file="cluster_result06.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
245 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
246 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
247 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
248 <param name="selected_algorithm" value="AffinityPropagation" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
249 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 34
diff changeset
250 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
251 <param name="col" value="2,3,4" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
252 <param name="damping" value="0.8" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
253 <output name="outfile" file="cluster_result07.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
254 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
255 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
256 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
257 <param name="selected_algorithm" value="MeanShift" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
258 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 34
diff changeset
259 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
260 <param name="col" value="2,3,4" />
34
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bgruening
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261 <param name="min_bin_freq" value="3" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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262 <output name="outfile" file="cluster_result08.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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263 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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264 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
265 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
266 <param name="selected_algorithm" value="MeanShift" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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267 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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268 <param name="header" value="false" />
13
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bgruening
parents: 0
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269 <param name="col" value="2,3,4" />
34
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bgruening
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270 <param name="cluster_all" value="False" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
271 <output name="outfile" file="cluster_result09.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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272 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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273 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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274 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
275 <param name="selected_algorithm" value="AgglomerativeClustering" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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276 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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277 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
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278 <param name="col" value="2,3,4" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
279 <param name="affinity" value="euclidean" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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280 <param name="linkage" value="average" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
281 <param name="n_clusters" value="4" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
282 <output name="outfile" file="cluster_result10.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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283 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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284 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
285 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
286 <param name="selected_algorithm" value="AgglomerativeClustering" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
287 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 34
diff changeset
288 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
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289 <param name="col" value="2,3,4" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
290 <param name="linkage" value="complete" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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291 <param name="n_clusters" value="4" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
292 <output name="outfile" file="cluster_result11.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
293 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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294 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
295 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
296 <param name="selected_algorithm" value="SpectralClustering" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
297 <param name="selected_input_type" value="tabular" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
298 <param name="col" value="2,3,4" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
299 <param name="header" value="false" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
300 <param name="eigen_solver" value="arpack" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
301 <param name="n_neighbors" value="12" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
302 <param name="n_clusters" value="4" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
303 <param name="assign_labels" value="discretize" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
304 <param name="random_state" value="100" />
23
9d234733ccfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
bgruening
parents: 21
diff changeset
305 <output name="outfile" file="cluster_result12.txt" compare="sim_size" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
306 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
307 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
308 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
309 <param name="selected_algorithm" value="SpectralClustering" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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diff changeset
310 <param name="selected_input_type" value="tabular" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
311 <param name="col" value="2,3,4" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
parents: 34
diff changeset
312 <param name="header" value="false" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
313 <param name="assign_labels" value="discretize" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
314 <param name="random_state" value="100" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
315 <param name="degree" value="2" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
316 <output name="outfile" file="cluster_result13.txt" compare="sim_size" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
317 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
318 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
319 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
320 <param name="selected_algorithm" value="MiniBatchKMeans" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
321 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
322 <param name="header" value="false" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
323 <param name="col" value="2,3,4" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
324 <param name="tol" value="0.5" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
325 <param name="random_state" value="100" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
326 <output name="outfile" file="cluster_result14.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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327 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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328 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
329 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
330 <param name="selected_algorithm" value="MiniBatchKMeans" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
331 <param name="selected_input_type" value="tabular" />
40
06d772036a62 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 9981e25b00de29ed881b2229a173a8c812ded9bb
bgruening
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diff changeset
332 <param name="header" value="false" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
333 <param name="n_init" value="5" />
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
bgruening
parents: 0
diff changeset
334 <param name="col" value="2,3,4" />
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
335 <param name="batch_size" value="10" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
336 <param name="n_clusters" value="4" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
337 <param name="random_state" value="100" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
338 <param name="reassignment_ratio" value="1.0" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
339 <output name="outfile" file="cluster_result15.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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340 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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341 <test>
34
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
342 <param name="infile" value="numeric_values.tabular" ftype="tabular" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
parents: 31
diff changeset
343 <param name="selected_algorithm" value="KMeans" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
bgruening
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344 <param name="selected_input_type" value="tabular" />
40
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345 <param name="header" value="false" />
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346 <param name="col" value="1" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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347 <param name="n_clusters" value="4" />
34
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348 <param name="random_state" value="100" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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349 <output name="outfile" file="cluster_result16.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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350 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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351 <test>
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352 <param name="infile" value="sparse.mtx" ftype="txt" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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353 <param name="selected_input_type" value="sparse" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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354 <param name="selected_algorithm" value="KMeans" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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355 <param name="n_clusters" value="2" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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356 <param name="init" value="k-means++" />
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357 <param name="random_state" value="100" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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358 <output name="outfile" file="cluster_result17.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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359 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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360 <test>
34
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361 <param name="infile" value="sparse.mtx" ftype="txt" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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362 <param name="selected_algorithm" value="DBSCAN" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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363 <param name="selected_input_type" value="sparse" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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364 <param name="algorithm" value="kd_tree" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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365 <param name="leaf_size" value="10" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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366 <param name="eps" value="1.0" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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367 <output name="outfile" file="cluster_result18.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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368 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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369 <test>
34
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370 <param name="infile" value="sparse.mtx" ftype="txt" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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371 <param name="selected_algorithm" value="Birch" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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372 <param name="selected_input_type" value="sparse" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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373 <param name="n_clusters" value="2" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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374 <param name="threshold" value="0.008" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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375 <output name="outfile" file="cluster_result19.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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376 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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377 <test>
34
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378 <param name="infile" value="sparse.mtx" ftype="txt" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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379 <param name="selected_algorithm" value="MiniBatchKMeans" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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380 <param name="selected_input_type" value="sparse" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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381 <param name="n_init" value="5" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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382 <param name="batch_size" value="10" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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383 <param name="n_clusters" value="2" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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384 <param name="random_state" value="100" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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385 <param name="reassignment_ratio" value="1.0" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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386 <output name="outfile" file="cluster_result20.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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387 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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388 <test>
34
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389 <param name="infile" value="sparse.mtx" ftype="txt" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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390 <param name="selected_algorithm" value="SpectralClustering" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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391 <param name="selected_input_type" value="sparse" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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392 <param name="assign_labels" value="discretize" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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393 <param name="n_clusters" value="2" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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394 <param name="random_state" value="100" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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395 <param name="degree" value="2" />
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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396 <output name="outfile" file="cluster_result21.txt" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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397 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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398 </tests>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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399 <help><![CDATA[
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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400 **What it does**
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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401 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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402 scikit-learn to find similarities among samples and cluster the samples based on these similarities.
34
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403 ]]> </help>
816b65d52c33 "planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit e2a5eade6d0e5ddf3a47630381a0ad90d80e8a04"
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404 <expand macro="sklearn_citation" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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405 </tool>