numeric_clustering: numeric_clustering.xml annotate

annotate numeric_clustering.xml @ 1:d645cdee08ed draft

planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0-dirty

author	bgruening
date	Fri, 01 Jan 2016 10:42:52 -0500
parents	42a2825313e9
children	1d465f2ebfad

rev	line source
0 42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	1 <tool id="numeric_clustering" name="Numeric Clustering" version="@VERSION@">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	2 <description></description>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	3 <requirements>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	4 <requirement type="package" version="2.3.0">anaconda</requirement>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	5 </requirements>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	6 <stdio>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	7 <exit_code level="fatal" range="1:"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	8 </stdio>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	9 <macros>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	10 <token name="@VERSION@">0.9</token>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	11 <macro name="n_clusters">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	12 <param name="n_clusters" type="integer" optional="true" value="8" label="Number of clusters"
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	13 help="default value is 8 (--n_clusters)"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	14 </macro>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	15 <macro name="n_init">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	16 <param name="n_init" type="integer" optional="true" value="" label="Number of runs with different centroid seeds"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	17 </macro>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	18 <macro name="max_iter">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	19 <param name="max_iter" type="integer" optional="true" value="" label="Maximum number of iterations per single run"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	20 </macro>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	21 <macro name="random_state">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	22 <param name="random_state" type="integer" optional="true" value="" label="Initialize centers"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	23 </macro>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	24 <macro name="affinity">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	25 <param name="affinity" type="text" optional="true" value="" label="Affinity"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	26 </macro>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	27 <macro name="tol">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	28 <param name="tol" type="float" optional="true" value="" label="Relative tolerance"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	29 </macro>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	30 <macro name="init">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	31 <param name="init" type="select" label="Select initialization method">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	32 <option value="k-means++">k-means++</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	33 <option value="random">random</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	34 </param>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	35 </macro>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	36 </macros>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	37 <version_command>echo "@VERSION@"</version_command>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	38 <command><![CDATA[
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	39 #import json
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	40 #set $params = dict()
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	41 #for $key, $value in $algorithm_options.items():
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	42 #if not $key.startswith('__') and $key.strip() != 'selected_algorithm' and str($value).strip():
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	43 #if str($value).strip() == 'false':
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	44 #set $value = False
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	45 #elif str($value).strip() == 'true':
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	46 #set $value = True
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	47 #else:
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	48 #try:
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	49 #set $val = float($value)
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	50 #try:
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	51 #set $value = int($value)
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	52 #except:
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	53 #set $value = float($value)
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	54 #end try
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	55 #except:
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	56 #set $value = str($value)
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	57 #end try
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	58 #end if
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	59 $params.update({str($key): $value})
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	60 #end if
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	61 #end for
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	62 #set $json_string = json.dumps( $params )
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	63
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	64 python "$cluster_script" '$json_string'
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	65 ]]>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	66 </command>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	67 <configfiles>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	68 <configfile name="cluster_script">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	69 <![CDATA[#!/usr/bin/env python
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	70 import sys
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	71 import json
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	72 import numpy as np
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	73 import sklearn.cluster
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	74 import pandas
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	75
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	76 data = pandas.DataFrame.from_csv("$infile", sep='\t', header=0, index_col=0, parse_dates=True, encoding=None, tupleize_cols=False )
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	77 my_class = getattr(sklearn.cluster, "$algorithm_options.selected_algorithm")
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	78 cluster_object = my_class()
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	79
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	80 params = json.loads( sys.argv[1] )
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	81 cluster_object.set_params(**params)
1 d645cdee08ed planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0-dirty bgruening parents: 0 diff changeset	82 if $end_column >= $start_column:
0 42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	83 data_matrix = data.values[:, $start_column-1:$end_column]
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	84 else:
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	85 data_matrix = data.values
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	86 prediction = cluster_object.fit_predict( data_matrix )
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	87 data['cluster_label'] = prediction
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	88 data.to_csv(path_or_buf = "$outfile",sep="\t")
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	89 ]]>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	90 </configfile>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	91 </configfiles>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	92 <inputs>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	93 <param name="infile" type="data" format="tabular" label="Data file with numeric values"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	94 <param name="start_column" label="Clustering column from" type="data_column" data_ref="infile" optional="True" />
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	95 <param name="end_column" label="to" type="data_column" data_ref="infile" optional="True" />
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	96 <conditional name="algorithm_options">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	97 <param name="selected_algorithm" type="select" label="Clustering Algorithm">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	98 <option value="KMeans">KMeans</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	99 <option value="DBSCAN">DBSCAN</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	100 <option value="Birch">Birch</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	101 <option value="MeanShift">MeanShift</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	102 <option value="AffinityPropagation">Affinity Propagation</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	103 <option value="AgglomerativeClustering">Agglomerative Clustering</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	104 <option value="SpectralClustering">Spectral Clustering</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	105 <option value="MiniBatchKMeans">Mini Batch KMeans</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	106 </param>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	107 <when value="KMeans">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	108 <expand macro="n_clusters"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	109 <expand macro="init"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	110 <expand macro="n_init"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	111 <expand macro="max_iter"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	112 <expand macro="tol"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	113 <param name="precompute_distances" type="text" optional="true" value="" label="Precompute distances"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	114 <expand macro="random_state"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	115 <param name="copy_x" type="boolean" optional="true" truevalue="--copy_x" falsevale="" label="Do not modify original data"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	116 </when>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	117 <when value="DBSCAN">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	118 <param name="eps" type="float" optional="true" value="0.5" label="Maximum neghborhood distance"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	119 <param name="min_samples" type="integer" optional="true" value="5" label="Core point minimum population"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	120 <param name="metric" type="text" optional="true" value="euclidean" label="Metric"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	121 <param name="algorithm" type="select" optional="true" value="auto" label="Pointwise distance algorithm">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	122 <option value="auto">auto</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	123 <option value="ball_tree">ball_tree</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	124 <option value="kd_tree">kd_tree</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	125 <option value="brute">brute</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	126 </param>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	127 <param name="leaf_size" type="integer" optional="true" value="30" label="Leaf size"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	128 </when>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	129 <when value="Birch">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	130 <param name="threshold" type="float" optional="true" value="0.5" label="Subcluster radius threshold"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	131 <param name="branching_factor" type="integer" optional="true" value="50" label="Maximum number of subclusters per branch"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	132 <expand macro="n_clusters"/> <!-- default to 3-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	133 <!--param name="compute_labels" type="boolean" optional="true" truevalue="true" falsevale="false" label="Compute labels for each fit"/-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	134 </when>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	135 <when value="AffinityPropagation">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	136 <param name="damping" type="float" optional="true" value="0.5" label="Damping factor"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	137 <expand macro="max_iter"/> <!--default to 200 -->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	138 <param name="convergence_iter" type="integer" optional="true" value="15" label="Number of iterations at each convergence step"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	139 <param name="copy" type="boolean" optional="true" truevalue="true" falsevale="false" label="Make a copy of input data"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	140 <!--param name="preference" type="text" optional="true" value="None" label="Array like shape (n_samples,)"/-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	141 <expand macro="affinity"/> <!--default = euclidean-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	142 </when>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	143 <when value="MeanShift">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	144 <param name="bandwidth" type="float" optional="true" value="" label="RBF kernel bandwidth"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	145 <!--param name="seeds" type="list" optional="true" value="None" label=""/-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	146 <param name="bin_seeding" type="boolean" optional="true" truevalue="true" falsevale="false" label="Discretize initial kernel locations"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	147 <param name="min_bin_freq" type="integer" optional="true" value="1" label="Minimum number of seeds per bin"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	148 <param name="cluster_all" type="boolean" optional="true" truevalue="true" falsevale="false" label="Cluster all"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	149 </when>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	150 <when value="AgglomerativeClustering">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	151 <expand macro="n_clusters"/> <!-- deafault 2-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	152 <expand macro="affinity"/> <!--default = euclidean-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	153 <!--param name="memory" type="callable" optional="true" value="Memory(cachedir=None)" label="Caching path"/-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	154 <!--param name="connectivity" type="list array-like or callable" optional="true" value="None" label="Connectivity matrix"/-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	155 <param name="n_components" type="integer" optional="true" value="" label="Number of connected components"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	156 <!--param name="compute_full_tree" type="text or boolean" optional="true" value="auto" label=""/-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	157 <param name="linkage" type="select" optional="true" value="ward" label="Linkage">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	158 <option value="ward">ward</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	159 <option value="complete">complete</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	160 <option value="average">average</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	161 </param>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	162 <!--param name="pooling_func" type="callable" optional="np.mean" value="None" label=""/-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	163 </when>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	164 <when value="SpectralClustering">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	165 <expand macro="n_clusters"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	166 <param name="eigen_solver" type="select" value="arpack" label="Eigenvalue decomposition strategy">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	167 <option value="arpack">arpack</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	168 <option value="lobpcg">lobpcg</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	169 <option value="amg">amg</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	170 </param>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	171 <expand macro="random_state"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	172 <!-- Todo: extend random_state type to int seed, RandomState instance, or None. -->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	173 <expand macro="n_init"/> <!-- default to 10-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	174 <param name="gamma" type="float" optional="true" value="1.0" label="Kernel scaling factor"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	175 <expand macro="affinity"/> <!--default =rbf-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	176 <param name="n_neighbors" type="integer" optional="true" value="10" label="Number of neighbors"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	177 <!--param name="eigen_tol" type="float" optional="true" value="0.0" label="arpack eigendecomposition stopping threshold"/-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	178 <param name="assign_labels" type="select" optional="true" value="kmeans" label="Assign labels">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	179 <option value="kmeans">kmeans</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	180 <option value="discretize">discretize</option>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	181 </param>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	182 <param name="degree" type="integer" optional="true" value="3" label="Degree of the polynomial (polynomial kernel only)"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	183 <param name="coef0" type="integer" optional="true" value="1" label="Zero coefficient (polynomial and sigmoid kernels only)"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	184 <!--param name="kernel_params" type="dict" optional="true" value="None" label=""/-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	185 </when>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	186 <when value="MiniBatchKMeans">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	187 <expand macro="n_clusters"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	188 <expand macro="init"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	189 <expand macro="n_init"/> <!-- default to 3-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	190 <expand macro="max_iter"/> <!--default to 100-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	191 <expand macro="tol"/> <!--default = 0.0-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	192 <expand macro="random_state"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	193 <param name="batch_size" type="integer" optional="true" value="100" label="Mini batch size"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	194 <!--param name="compute_labels" type="boolean" optional="true" truevalue="true" falsevale="false" label="Compute labels for all data"/-->
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	195 <param name="max_no_improvement" type="integer" optional="true" value="10" label="Maximum number of improvement attempts"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	196 <param name="init_size" type="integer" optional="true" value="" label="Number of random init samples"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	197 <param name="reassignment_ratio" type="float" optional="true" value="0.01" label="Re-assignment ratio"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	198 </when>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	199 </conditional>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	200 </inputs>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	201 <outputs>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	202 <data format_source="infile" name="outfile"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	203 </outputs>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	204 <tests>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	205 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	206 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	207 <param name="selected_algorithm" value="KMeans"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	208 <param name="n_clusters" value="4" />
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	209 <param name="init" value="k-means++" />
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	210 <param name="random_state" value="100"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	211 <output name="outfile" file="cluster_result01.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	212 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	213 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	214 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	215 <param name="selected_algorithm" value="KMeans"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	216 <param name="n_clusters" value="6" />
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	217 <param name="init" value="random" />
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	218 <param name="random_state" value="100"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	219 <output name="outfile" file="cluster_result02.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	220 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	221 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	222 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	223 <param name="selected_algorithm" value="DBSCAN"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	224 <param name="algorithm" value="kd_tree"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	225 <param name="leaf_size" value="10"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	226 <param name="eps" value="1.0"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	227 <output name="outfile" file="cluster_result03.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	228 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	229 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	230 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	231 <param name="selected_algorithm" value="Birch"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	232 <param name="n_clusters" value="5"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	233 <param name="threshold" value="0.008"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	234 <output name="outfile" file="cluster_result04.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	235 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	236 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	237 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	238 <param name="selected_algorithm" value="Birch"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	239 <param name="branching_factor" value="20"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	240 <output name="outfile" file="cluster_result05.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	241 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	242 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	243 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	244 <param name="selected_algorithm" value="AffinityPropagation"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	245 <param name="affinity" value="euclidean"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	246 <param name="copy" value="false"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	247 <output name="outfile" file="cluster_result06.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	248 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	249 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	250 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	251 <param name="selected_algorithm" value="AffinityPropagation"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	252 <param name="damping" value="0.8"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	253 <output name="outfile" file="cluster_result07.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	254 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	255 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	256 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	257 <param name="selected_algorithm" value="MeanShift"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	258 <param name="min_bin_freq" value="3"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	259 <output name="outfile" file="cluster_result08.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	260 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	261 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	262 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	263 <param name="selected_algorithm" value="MeanShift"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	264 <param name="cluster_all" value="False"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	265 <output name="outfile" file="cluster_result09.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	266 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	267 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	268 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	269 <param name="selected_algorithm" value="AgglomerativeClustering"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	270 <param name="affinity" value="euclidean"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	271 <param name="linkage" value="average"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	272 <output name="outfile" file="cluster_result10.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	273 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	274 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	275 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	276 <param name="selected_algorithm" value="AgglomerativeClustering"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	277 <param name="linkage" value="complete"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	278 <param name="n_clusters" value="5"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	279 <output name="outfile" file="cluster_result11.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	280 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	281 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	282 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	283 <param name="selected_algorithm" value="SpectralClustering"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	284 <param name="eigen_solver" value="arpack"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	285 <param name="n_neighbors" value="12"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	286 <param name="n_clusters" value="7"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	287 <param name="assign_labels" value="discretize"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	288 <param name="random_state" value="100"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	289 <output name="outfile" file="cluster_result12.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	290 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	291 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	292 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	293 <param name="selected_algorithm" value="SpectralClustering"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	294 <param name="assign_labels" value="discretize"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	295 <param name="random_state" value="100"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	296 <param name="degree" value="2"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	297 <output name="outfile" file="cluster_result13.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	298 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	299 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	300 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	301 <param name="selected_algorithm" value="MiniBatchKMeans"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	302 <param name="tol" value="0.5"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	303 <param name="random_state" value="100"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	304 <output name="outfile" file="cluster_result14.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	305 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	306 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	307 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	308 <param name="selected_algorithm" value="MiniBatchKMeans"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	309 <param name="n_init" value="5"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	310 <param name="batch_size" value="10"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	311 <param name="n_clusters" value="3"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	312 <param name="random_state" value="100"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	313 <param name="reassignment_ratio" value="1.0"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	314 <output name="outfile" file="cluster_result15.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	315 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	316 <test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	317 <param name="infile" value="numeric_values.tabular" ftype="tabular"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	318 <param name="selected_algorithm" value="KMeans"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	319 <param name="start_column" value="3" />
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	320 <param name="end_column" value="4" />
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	321 <param name="n_clusters" value="6" />
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	322 <param name="init" value="random" />
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	323 <param name="random_state" value="100"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	324 <output name="outfile" file="cluster_result16.txt"/>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	325 </test>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	326 </tests>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	327 <help><![CDATA[
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	328 What it does
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	329
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	330 This clustering tool offers different clustering algorithms which are provided by
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	331 scikit-learn to find similarities among samples and cluster the samples based on these similarities.
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	332
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	333 ]]></help>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	334 <citations>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	335 <citation type="bibtex">
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	336 @article{scikit-learn,
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	337 title={Scikit-learn: Machine Learning in {P}ython},
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	338 author={Pedregosa, F. and Varoquaux, G. and Gramfort, A. and Michel, V.
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	339 and Thirion, B. and Grisel, O. and Blondel, M. and Prettenhofer, P.
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	340 and Weiss, R. and Dubourg, V. and Vanderplas, J. and Passos, A. and
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	341 Cournapeau, D. and Brucher, M. and Perrot, M. and Duchesnay, E.},
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	342 journal={Journal of Machine Learning Research},
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	343 volume={12},
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	344 pages={2825--2830},
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	345 year={2011}
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	346 url = {https://github.com/scikit-learn/scikit-learn}
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	347 }
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	348 </citation>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	349 </citations>
42a2825313e9 planemo upload for repository https://github.com/bgruening/galaxytools/tree/master/tools/numeric_clustering commit ac9beb7e9c83b0ae811b304eb3085a4b0930f5a0 bgruening parents: diff changeset	350 </tool>

Mercurial > repos > bgruening > numeric_clustering

annotate numeric_clustering.xml @ 1:d645cdee08ed draft