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1 <tool id="cluster3" name="Cluster 3" version="1.0.0">
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2 <description>Cluster 3.0</description>
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3 <command interpreter="python">$scriptfile</command>
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4 <inputs>
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5 <param name="filename" type="data" format="tab" label="Matrix"/>
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6 <param name="row_center" type="select" label="Row Center (gene)">
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7 <option value="x">No row Center</option>
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8 <option value="a">Substact mean of row</option>
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9 <option value="m">Substact median of row</option>
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10 </param>
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11 <param name="log_transform" type="boolean" label="Log transform data" default="false"/>
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12 <param name="row_normalize" type="boolean" label="Normalize Rows (gene)"/>
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13
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14 <param name="col_center" type="select" label="Column Center (sample)">
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15 <option value="x">No column Center</option>
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16 <option value="a">Substact mean of column</option>
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17 <option value="m">Substact median of column</option>
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18 </param>
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19 <param name="col_normalize" type="boolean" label="Normalize Columns (sample)"/>
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20
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21
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22 <param name="col_algorithm" type="select" label="Column (sample) clustering">
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23 <option value="0">No clustering</option>
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24 <option value="1">Uncentered correlation</option>
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25 <option value="2">Pearson correlation</option>
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26 <option value="3">Uncentered correlation, absolute value</option>
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27 <option value="4">Pearson correlation, absolute value</option>
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28 <option value="5">Spearman's rank correlation</option>
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29 <option value="6">Kendall's tau</option>
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30 <option value="7">Euclidean distance</option>
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31 <option value="8">City-block distance</option>
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32 </param>
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33
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34 <param name="row_algorithm" type="select" label="Row (gene) clustering">
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35 <option value="0">No clustering</option>
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36 <option value="1">Uncentered correlation</option>
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37 <option value="2">Pearson correlation</option>
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38 <option value="3">Uncentered correlation, absolute value</option>
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39 <option value="4">Pearson correlation, absolute value</option>
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40 <option value="5">Spearman's rank correlation</option>
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41 <option value="6">Kendall's tau</option>
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42 <option value="7">Euclidean distance</option>
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43 <option value="8">City-block distance</option>
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44 </param>
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45
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46 <param name="hclustermethod" type="select" label="Hierarchical clustering method">
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47 <option value="x">Off</option>
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48 <option value="m">Pairwise complete-linkage</option>
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49 <option value="s">Pairwise single-linkage</option>
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50 <option value="c">Pairwise centroid-linkage</option>
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51 <option value="a">Pairwise average-linkage</option>
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52 </param>
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53
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54 <param name="knum" type="integer" optional="true" label="K-Means count"/>
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55 <param name="kcount" type="integer" optional="true" label="K-Means run count"/>
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56
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57 <param name="prow" type="boolean" label="Principal Component Analysis to rows (genes) instead of clustering"/>
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58 <param name="pcol" type="boolean" label="Principal Component Analysis to cols (samples) instead of clustering"/>
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59
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60
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61 </inputs>
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62 <outputs>
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63 <data name="cdtfile" format="cdt"/>
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64 <data format="atr" name="atrfile" >
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65 <filter>col_algorithm != "0"</filter>
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66 </data>
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67 <data format="atr" name="atrfile" >
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68 <filter>col_algorithm != "0"</filter>
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69 </data>
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70 <data format="gtr" name="gtrfile" >
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71 <filter>row_algorithm != "0"</filter>
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72 </data>
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73 </outputs>
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74 <configfiles>
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75
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76 <configfile name="scriptfile"><![CDATA[#!/usr/bin/env python
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77 import subprocess
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78 import shutil
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79
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80 cmd = ["cluster", "-f", "$filename", "-u", "galaxy_cluster"]
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81
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82 if "$col_algorithm" != "0":
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83 cmd.extend( ['-e', '$col_algorithm'] )
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84
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85 if "$row_algorithm" != "0":
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86 cmd.extend( ['-g', '$row_algorithm'] )
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87
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88 if len("$knum"):
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89 cmd.extend(['-k', '$knum'])
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90
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91 if len("$kcount"):
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92 cmd.extend(['-k', '$kcount'])
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93
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94 if "$col_normalize" == "true":
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95 cmd.append("-na")
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96
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97 if "$row_normalize" == "true":
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98 cmd.append("-ng")
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99
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100 if "$log_transform" == "true":
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101 cmd.append("-l")
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102
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103 print cmd
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104
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105 proc = subprocess.Popen(cmd)
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106 proc.communicate()
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107
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108 shutil.move("galaxy_cluster" + ".cdt", "$cdtfile")
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109
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110 if "$col_algorithm" != "0":
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111 shutil.move("galaxy_cluster" + ".atr", "$atrfile")
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112
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113 if "$row_algorithm" != "0":
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114 shutil.move("galaxy_cluster" + ".gtr", "$gtrfile")
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115
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116
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117 ]]></configfile>
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118 </configfiles>
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119 <help>
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120
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121 A Wrapper for the Cluster3.0 library http://bonsai.hgc.jp/~mdehoon/software/cluster/software.htm
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122
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123 Source code at http://bonsai.hgc.jp/~mdehoon/software/cluster/cluster-1.50.tar.gz
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124
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125 For command line version,
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126 ./configure --without-x
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127 make
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128 make install
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129
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130 </help>
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131 </tool>
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