Mercurial > repos > bgruening > sklearn_numeric_clustering

annotate numeric_clustering.xml @ 24:abb5a3f256e3 draft

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planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit c0a3a186966888e5787335a7628bf0a4382637e7
author bgruening
date Tue, 14 May 2019 18:11:02 -0400
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children 37e193b3fdd7
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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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24
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25 sys.path.insert(0, '$__tool_directory__')
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26 from 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 #if $input_types.selected_input_type == "sparse":
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46 data_matrix = mmread("$infile")
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47 #else:
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48 data = pandas.read_csv("$infile", sep='\t', header=0, index_col=None, parse_dates=True, encoding=None, tupleize_cols=False )
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49 header = 'infer' if params["input_types"]["header"] else None
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50 column_option = params["input_types"]["column_selector_options"]["selected_column_selector_option"]
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51 if column_option in ["by_index_number", "all_but_by_index_number", "by_header_name", "all_but_by_header_name"]:
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52 c = params["input_types"]["column_selector_options"]["col"]
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53 else:
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54 c = None
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55 data_matrix = read_columns(
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56 "$infile",
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57 c = c,
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58 c_option = column_option,
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59 sep='\t',
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60 header=header,
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61 parse_dates=True,
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62 encoding=None,
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63 tupleize_cols=False)
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64 #end if
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65
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66 prediction = cluster_object.fit_predict( data_matrix )
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67
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68 if len(np.unique(prediction)) > 1:
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69 silhouette_score = metrics.silhouette_score(data_matrix,prediction,metric='euclidean')
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70 else:
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71 silhouette_score = -1
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72 sys.stdout.write('silhouette score:' + '\t' + str(silhouette_score) + '\n')
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73
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74 prediction_df = pandas.DataFrame(prediction, columns=["predicted"])
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75
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76 #if $input_types.selected_input_type == "sparse":
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77 res = prediction_df
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78 #else:
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79 res = pandas.concat([data, prediction_df], axis=1)
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80 #end if
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81
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82 res.to_csv(path_or_buf = "$outfile", sep="\t", index=False, header=False)
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83 ]]>
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84 </configfile>
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85 </configfiles>
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86 <inputs>
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87 <conditional name="input_types">
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88 <param name="selected_input_type" type="select" label="Select the format of input data">
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89 <option value="tabular" selected="true">Tabular Format (tabular, txt)</option>
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90 <option value="sparse">Sparse Vector Representation (mtx)</option>
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91 </param>
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92 <when value="sparse">
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93 <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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94 <expand macro="clustering_algorithms_options"/>
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95 </when>
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96 <when value="tabular">
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97 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
13
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98 <param name="header" type="boolean" optional="true" truevalue="booltrue" falsevalue="boolfalse" checked="True" label="Does the dataset contain header:" />
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99 <conditional name="column_selector_options">
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100 <expand macro="samples_column_selector_options" col_name="col" multiple="true" infile="infile"/>
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101 </conditional>
0
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102 <!--expand macro="clustering_algorithms_options"-->
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103 <conditional name="algorithm_options">
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104 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
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105 <option value="AgglomerativeClustering">Hierarchical Agglomerative Clustering</option>
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106 <option value="AffinityPropagation">Affinity Propagation</option>
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107 <option value="SpectralClustering">Spectral Clustering</option>
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108 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
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109 <option value="MeanShift">MeanShift</option>
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110 <option value="KMeans">KMeans</option>
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111 <option value="DBSCAN">DBSCAN</option>
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112 <option value="Birch">Birch</option>
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113 </param>
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114 <when value="KMeans">
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115 <expand macro="kmeans_advanced_options"/>
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116 </when>
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117 <when value="DBSCAN">
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118 <expand macro="dbscan_advanced_options"/>
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119 </when>
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120 <when value="Birch">
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121 <expand macro="birch_advanced_options"/>
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122 </when>
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123 <when value="SpectralClustering">
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124 <expand macro="spectral_clustering_advanced_options"/>
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125 </when>
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126 <when value="MiniBatchKMeans">
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127 <expand macro="minibatch_kmeans_advanced_options"/>
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128 </when>
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129 <when value="AffinityPropagation">
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130 <section name="options" title="Advanced Options" expanded="False">
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131 <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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132 <expand macro="max_iter" default_value="200"/>
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133 <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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134 <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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135 <!--param argument="preference"/-->
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136 <param argument="affinity" type="select" label="Affinity" help="Affinity to use; euclidean uses the negative squared euclidean distance between points.">
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137 <option value="euclidean">Euclidean</option>
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138 <option value="precomputed">precomputed</option>
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139 </param>
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140 </section>
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141 </when>
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142 <when value="MeanShift">
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143 <section name="options" title="Advanced Options" expanded="False">
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144 <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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145 <!--param argument="seeds"/-->
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146 <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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147 <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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148 <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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149 </section>
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150 </when>
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151 <when value="AgglomerativeClustering">
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152 <section name="options" title="Advanced Options" expanded="False">
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153 <expand macro="n_clusters" default_value="2" />
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154 <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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155 <option value="euclidean">Euclidean</option>
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156 <option value="manhattan">Manhattan</option>
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157 <option value="l1">L1</option>
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158 <option value="l2">L2</option>
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159 <option value="cosine">cosine</option>
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160 <option value="precomputed">precomputed</option>
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161 </param>
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162 <!--param argument="memory"-->
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163 <!--param argument="connectivity"-->
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164 <!--param argument="n_components"/-->
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165 <!--param argument="compute_full_tree"-->
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166 <param argument="linkage" type="select" optional="true" label="Linkage" help="">
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167 <option value="ward" selected="true">ward</option>
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168 <option value="complete">complete</option>
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169 <option value="average">average</option>
23
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170 <option value="single">single</option>
0
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171 </param>
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172 <!--param argument="pooling_func"-->
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173 </section>
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174 </when>
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175 </conditional>
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176 </when>
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177 </conditional>
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178 </inputs>
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179 <outputs>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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180 <data format="tabular" name="outfile"/>
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181 </outputs>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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182 <tests>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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183 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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184 <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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185 <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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186 <param name="selected_algorithm" value="KMeans"/>
13
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187 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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188 <param name="n_clusters" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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189 <param name="init" value="k-means++" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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190 <param name="random_state" value="100"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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191 <output name="outfile" file="cluster_result01.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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192 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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193 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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194 <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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195 <param name="selected_algorithm" value="KMeans"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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196 <param name="selected_input_type" value="tabular"/>
13
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197 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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198 <param name="n_clusters" value="4" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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199 <param name="init" value="random" />
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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200 <param name="random_state" value="100"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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201 <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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202 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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203 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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204 <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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205 <param name="selected_algorithm" value="DBSCAN"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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206 <param name="selected_input_type" value="tabular"/>
13
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diff changeset
207 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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208 <param name="algorithm" value="kd_tree"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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209 <param name="leaf_size" value="10"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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210 <param name="eps" value="1.0"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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211 <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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212 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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213 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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214 <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
215 <param name="selected_algorithm" value="Birch"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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216 <param name="selected_input_type" value="tabular"/>
13
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diff changeset
217 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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218 <param name="n_clusters" value="4"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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219 <param name="threshold" value="0.008"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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220 <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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221 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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222 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
223 <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
224 <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
225 <param name="selected_input_type" value="tabular"/>
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
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diff changeset
226 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
227 <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
228 <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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229 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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230 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
231 <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
232 <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
233 <param name="selected_input_type" value="tabular"/>
13
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diff changeset
234 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
235 <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
236 <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
237 <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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238 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
239 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
240 <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
241 <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
242 <param name="selected_input_type" value="tabular"/>
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
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diff changeset
243 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
244 <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
245 <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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246 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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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"/>
13
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diff changeset
251 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
252 <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
253 <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
254 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
255 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
256 <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
257 <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
258 <param name="selected_input_type" value="tabular"/>
13
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diff changeset
259 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
260 <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
261 <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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262 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
263 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
264 <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
265 <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
266 <param name="selected_input_type" value="tabular"/>
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
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diff changeset
267 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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268 <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
269 <param name="linkage" value="average"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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270 <param name="n_clusters" value="4"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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271 <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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272 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
273 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
274 <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
275 <param name="selected_algorithm" value="AgglomerativeClustering"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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276 <param name="selected_input_type" value="tabular"/>
13
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diff changeset
277 <param name="col" value="2,3,4" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
278 <param name="linkage" value="complete"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
279 <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
280 <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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diff changeset
281 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
282 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
283 <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
284 <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
285 <param name="selected_input_type" value="tabular"/>
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
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diff changeset
286 <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
287 <param name="eigen_solver" value="arpack"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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288 <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
289 <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
290 <param name="assign_labels" value="discretize"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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291 <param name="random_state" value="100"/>
23
9d234733ccfd planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 57f4407e278a615f47a377a3328782b1d8e0b54d
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diff changeset
292 <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
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293 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
294 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
295 <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
296 <param name="selected_algorithm" value="SpectralClustering"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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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
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parents: 0
diff changeset
298 <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
299 <param name="assign_labels" value="discretize"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
300 <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
301 <param name="degree" value="2"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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302 <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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diff changeset
303 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
304 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
305 <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
306 <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
307 <param name="selected_input_type" value="tabular"/>
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
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parents: 0
diff changeset
308 <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
309 <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
310 <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
311 <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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diff changeset
312 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
313 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
314 <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
315 <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
316 <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
317 <param name="n_init" value="5"/>
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
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parents: 0
diff changeset
318 <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
319 <param name="batch_size" value="10"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
320 <param name="n_clusters" value="4"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
diff changeset
321 <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
322 <param name="reassignment_ratio" value="1.0"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
323 <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
324 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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diff changeset
325 <test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
326 <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
327 <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
328 <param name="selected_input_type" value="tabular"/>
13
40f3318b61c2 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/sklearn commit 5d71c93a3dd804b1469852240a86021ab9130364
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parents: 0
diff changeset
329 <param name="col" value="1" />
0
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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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
bgruening
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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
bgruening
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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
bgruening
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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
bgruening
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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
bgruening
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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
bgruening
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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
bgruening
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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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diff changeset
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
bgruening
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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
bgruening
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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
bgruening
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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
bgruening
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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
bgruening
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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
parents:
diff changeset
350 <output name="outfile" file="cluster_result18.txt"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
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diff changeset
351 </test>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
bgruening
parents:
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
parents:
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
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356 <param name="n_clusters" value="2"/>
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357 <param name="threshold" value="0.008"/>
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358 <output name="outfile" file="cluster_result19.txt"/>
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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"/>
c7b8fab00c0f planemo upload for repository https://github.com/bgruening/galaxytools/tools/sklearn commit 0e582cf1f3134c777cce3aa57d71b80ed95e6ba9
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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"/>
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368 <param name="reassignment_ratio" value="1.0"/>
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369 <output name="outfile" file="cluster_result20.txt"/>
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370 </test>
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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"/>
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373 <param name="selected_algorithm" value="SpectralClustering"/>
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374 <param name="selected_input_type" value="sparse"/>
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375 <param name="assign_labels" value="discretize"/>
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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"/>
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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>