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1 <?xml version="1.0" ?>
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2 <tool id="qiime_feature-table_heatmap" name="qiime feature-table heatmap"
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3 version="2020.8">
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4 <description>Generate a heatmap representation of a feature table</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime feature-table heatmap
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10
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11 --i-table=$itable
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12 # if $input_files_msamplemetadatafile:
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13 # def list_dict_to_string(list_dict):
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14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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15 # for d in list_dict[1:]:
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16 # set $file_list = $file_list + ' --m-sample-metadata-file=' + d['additional_input'].__getattr__('file_name')
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17 # end for
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18 # return $file_list
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19 # end def
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20 --m-sample-metadata-file=$list_dict_to_string($input_files_msamplemetadatafile)
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21 # end if
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22
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23 #if '__ob__' in str($msamplemetadatacolumn):
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24 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__ob__', '[')
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25 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
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26 #end if
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27 #if '__cb__' in str($msamplemetadatacolumn):
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28 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__cb__', ']')
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29 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
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30 #end if
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31 #if 'X' in str($msamplemetadatacolumn):
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32 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('X', '\\')
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33 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
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34 #end if
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35 #if '__sq__' in str($msamplemetadatacolumn):
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36 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__sq__', "'")
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37 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
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38 #end if
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39 #if '__db__' in str($msamplemetadatacolumn):
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40 #set $msamplemetadatacolumn_temp = $msamplemetadatacolumn.replace('__db__', '"')
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41 #set $msamplemetadatacolumn = $msamplemetadatacolumn_temp
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42 #end if
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43
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44 #if str($msamplemetadatacolumn):
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45 --m-sample-metadata-column=$msamplemetadatacolumn
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46 #end if
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47 # if $input_files_mfeaturemetadatafile:
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48 # def list_dict_to_string(list_dict):
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49 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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50 # for d in list_dict[1:]:
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51 # set $file_list = $file_list + ' --m-feature-metadata-file=' + d['additional_input'].__getattr__('file_name')
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52 # end for
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53 # return $file_list
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54 # end def
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55 --m-feature-metadata-file=$list_dict_to_string($input_files_mfeaturemetadatafile)
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56 # end if
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57
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58 #if '__ob__' in str($mfeaturemetadatacolumn):
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59 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__ob__', '[')
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60 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
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61 #end if
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62 #if '__cb__' in str($mfeaturemetadatacolumn):
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63 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__cb__', ']')
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64 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
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65 #end if
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66 #if 'X' in str($mfeaturemetadatacolumn):
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67 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('X', '\\')
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68 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
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69 #end if
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70 #if '__sq__' in str($mfeaturemetadatacolumn):
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71 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__sq__', "'")
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72 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
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73 #end if
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74 #if '__db__' in str($mfeaturemetadatacolumn):
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75 #set $mfeaturemetadatacolumn_temp = $mfeaturemetadatacolumn.replace('__db__', '"')
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76 #set $mfeaturemetadatacolumn = $mfeaturemetadatacolumn_temp
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77 #end if
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78
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79 #if str($mfeaturemetadatacolumn):
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80 --m-feature-metadata-column=$mfeaturemetadatacolumn
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81 #end if
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82
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83 #if $pnonormalize:
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84 --p-no-normalize
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85 #end if
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86
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87 #if str($ptitle):
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88 --p-title=$ptitle
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89 #end if
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90 #if str($pmetric) != 'None':
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91 --p-metric=$pmetric
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92 #end if
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93
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94 #if str($pmethod) != 'None':
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95 --p-method=$pmethod
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96 #end if
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97
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98 #if str($pcluster) != 'None':
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99 --p-cluster=$pcluster
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100 #end if
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101
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102 #if str($pcolorscheme) != 'None':
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103 --p-color-scheme=$pcolorscheme
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104 #end if
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105
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106 --o-visualization=ovisualization
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107
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108 #if str($examples) != 'None':
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109 --examples=$examples
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110 #end if
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111
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112 ;
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113 cp ogroupedtable.qza $ogroupedtable
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114
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115 ;
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116 qiime tools export ovisualization.qzv --output-path out
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117 && mkdir -p '$ovisualization.files_path'
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118 && cp -r out/* '$ovisualization.files_path'
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119 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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120
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121 ]]></command>
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122 <inputs>
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123 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table to visualize. [required]" name="itable" optional="False" type="data" />
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124 <repeat name="input_files_msamplemetadatafile" optional="True" title="--m-sample-metadata-file">
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125 <param format="tabular,qza,no_unzip.zip" label="--m-sample-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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126 </repeat>
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127 <param label="--m-sample-metadata-column: COLUMN MetadataColumn[Categorical] Annotate the sample IDs with these sample metadata values. When metadata is present and `cluster`=\'feature\', samples will be sorted by the metadata values. [optional]" name="msamplemetadatacolumn" optional="False" type="text" />
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128 <repeat name="input_files_mfeaturemetadatafile" optional="True" title="--m-feature-metadata-file">
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129 <param format="tabular,qza,no_unzip.zip" label="--m-feature-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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130 </repeat>
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131 <param label="--m-feature-metadata-column: COLUMN MetadataColumn[Categorical] Annotate the feature IDs with these feature metadata values. When metadata is present and `cluster`=\'sample\', features will be sorted by the metadata values. [optional]" name="mfeaturemetadatacolumn" optional="False" type="text" />
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132 <param label="--p-no-normalize: Do not normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table. [default: True]" name="pnonormalize" selected="False" type="boolean" />
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133 <param label="--p-title: TEXT Optional custom plot title. [optional]" name="ptitle" optional="False" type="text" />
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134 <param label="--p-metric: " name="pmetric" optional="True" type="select">
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135 <option selected="True" value="None">Selection is Optional</option>
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136 <option value="euclidean">euclidean</option>
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137 <option value="cityblock">cityblock</option>
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138 <option value="matching">matching</option>
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139 <option value="russellrao">russellrao</option>
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140 <option value="sokalmichener">sokalmichener</option>
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141 <option value="kulsinski">kulsinski</option>
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142 <option value="chebyshev">chebyshev</option>
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143 <option value="hamming">hamming</option>
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144 <option value="dice">dice</option>
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145 <option value="yule">yule</option>
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146 <option value="rogerstanimoto">rogerstanimoto</option>
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147 <option value="braycurtis">braycurtis</option>
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148 <option value="cosine">cosine</option>
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149 <option value="minkowski">minkowski</option>
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150 <option value="correlation">correlation</option>
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151 <option value="sokalsneath">sokalsneath</option>
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152 <option value="seuclidean">seuclidean</option>
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153 <option value="canberra">canberra</option>
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154 <option value="mahalanobis">mahalanobis</option>
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155 <option value="jaccard">jaccard</option>
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156 <option value="sqeuclidean">sqeuclidean</option>
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157 </param>
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158 <param label="--p-method: " name="pmethod" optional="True" type="select">
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159 <option selected="True" value="None">Selection is Optional</option>
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160 <option value="centroid">centroid</option>
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161 <option value="median">median</option>
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162 <option value="weighted">weighted</option>
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163 <option value="average">average</option>
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164 <option value="single">single</option>
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165 <option value="complete">complete</option>
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166 <option value="ward">ward</option>
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167 </param>
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168 <param label="--p-cluster: " name="pcluster" optional="True" type="select">
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169 <option selected="True" value="None">Selection is Optional</option>
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170 <option value="both">both</option>
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171 <option value="none">none</option>
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172 <option value="features">features</option>
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173 <option value="samples">samples</option>
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174 </param>
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175 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
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176 <option selected="True" value="None">Selection is Optional</option>
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177 <option value="Spectral">Spectral</option>
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178 <option value="flag">flag</option>
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179 <option value="jet">jet</option>
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180 <option value="Vega20">Vega20</option>
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181 <option value="terrain">terrain</option>
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182 <option value="jet_r">jet_r</option>
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183 <option value="Vega20c_r">Vega20c_r</option>
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184 <option value="Oranges_r">Oranges_r</option>
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185 <option value="spectral">spectral</option>
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186 <option value="summer">summer</option>
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187 <option value="BuPu_r">BuPu_r</option>
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188 <option value="tab20b_r">tab20b_r</option>
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189 <option value="Pastel1">Pastel1</option>
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190 <option value="gnuplot_r">gnuplot_r</option>
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191 <option value="seismic">seismic</option>
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192 <option value="icefire">icefire</option>
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193 <option value="Set1">Set1</option>
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194 <option value="bwr">bwr</option>
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195 <option value="coolwarm_r">coolwarm_r</option>
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196 <option value="ocean_r">ocean_r</option>
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197 <option value="gist_gray_r">gist_gray_r</option>
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198 <option value="autumn">autumn</option>
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199 <option value="BrBG">BrBG</option>
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200 <option value="Pastel2">Pastel2</option>
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201 <option value="GnBu">GnBu</option>
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202 <option value="Vega20b_r">Vega20b_r</option>
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203 <option value="tab20c">tab20c</option>
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204 <option value="Paired">Paired</option>
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205 <option value="YlOrRd_r">YlOrRd_r</option>
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206 <option value="icefire_r">icefire_r</option>
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207 <option value="cubehelix_r">cubehelix_r</option>
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208 <option value="CMRmap_r">CMRmap_r</option>
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209 <option value="RdBu">RdBu</option>
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210 <option value="YlGn_r">YlGn_r</option>
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211 <option value="gray_r">gray_r</option>
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212 <option value="mako_r">mako_r</option>
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213 <option value="OrRd_r">OrRd_r</option>
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214 <option value="Vega10">Vega10</option>
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215 <option value="Set3">Set3</option>
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216 <option value="RdYlGn_r">RdYlGn_r</option>
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217 <option value="hsv">hsv</option>
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218 <option value="cool_r">cool_r</option>
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219 <option value="Spectral_r">Spectral_r</option>
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220 <option value="rainbow">rainbow</option>
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221 <option value="cividis">cividis</option>
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222 <option value="Blues_r">Blues_r</option>
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223 <option value="PuOr_r">PuOr_r</option>
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224 <option value="binary_r">binary_r</option>
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225 <option value="RdGy">RdGy</option>
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226 <option value="Pastel2_r">Pastel2_r</option>
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227 <option value="Pastel1_r">Pastel1_r</option>
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228 <option value="Dark2">Dark2</option>
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229 <option value="vlag">vlag</option>
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230 <option value="binary">binary</option>
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231 <option value="pink">pink</option>
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232 <option value="Purples">Purples</option>
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233 <option value="cividis_r">cividis_r</option>
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234 <option value="gray">gray</option>
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235 <option value="seismic_r">seismic_r</option>
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236 <option value="Greys">Greys</option>
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237 <option value="tab20">tab20</option>
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238 <option value="BuPu">BuPu</option>
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239 <option value="RdBu_r">RdBu_r</option>
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240 <option value="gnuplot2_r">gnuplot2_r</option>
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241 <option value="Accent_r">Accent_r</option>
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242 <option value="magma">magma</option>
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243 <option value="copper_r">copper_r</option>
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244 <option value="inferno">inferno</option>
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245 <option value="nipy_spectral_r">nipy_spectral_r</option>
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246 <option value="pink_r">pink_r</option>
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247 <option value="copper">copper</option>
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248 <option value="Dark2_r">Dark2_r</option>
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249 <option value="YlGnBu_r">YlGnBu_r</option>
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250 <option value="Wistia_r">Wistia_r</option>
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251 <option value="spectral_r">spectral_r</option>
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252 <option value="cubehelix">cubehelix</option>
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253 <option value="tab20_r">tab20_r</option>
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254 <option value="viridis">viridis</option>
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255 <option value="RdYlBu">RdYlBu</option>
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256 <option value="Blues">Blues</option>
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257 <option value="rocket_r">rocket_r</option>
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258 <option value="Set1_r">Set1_r</option>
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259 <option value="brg_r">brg_r</option>
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260 <option value="bone_r">bone_r</option>
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261 <option value="gist_ncar_r">gist_ncar_r</option>
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262 <option value="afmhot">afmhot</option>
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263 <option value="RdYlBu_r">RdYlBu_r</option>
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264 <option value="gist_earth_r">gist_earth_r</option>
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265 <option value="RdGy_r">RdGy_r</option>
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266 <option value="Vega10_r">Vega10_r</option>
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267 <option value="gist_rainbow_r">gist_rainbow_r</option>
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268 <option value="spring">spring</option>
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269 <option value="Set3_r">Set3_r</option>
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270 <option value="magma_r">magma_r</option>
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271 <option value="mako">mako</option>
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272 <option value="PuRd">PuRd</option>
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273 <option value="gnuplot2">gnuplot2</option>
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274 <option value="Paired_r">Paired_r</option>
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275 <option value="Vega20b">Vega20b</option>
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276 <option value="Accent">Accent</option>
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277 <option value="hsv_r">hsv_r</option>
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278 <option value="ocean">ocean</option>
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279 <option value="gist_earth">gist_earth</option>
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280 <option value="afmhot_r">afmhot_r</option>
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281 <option value="bone">bone</option>
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282 <option value="rocket">rocket</option>
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283 <option value="RdYlGn">RdYlGn</option>
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284 <option value="bwr_r">bwr_r</option>
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285 <option value="RdPu_r">RdPu_r</option>
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286 <option value="BuGn">BuGn</option>
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287 <option value="PuBu">PuBu</option>
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288 <option value="hot_r">hot_r</option>
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289 <option value="Vega20c">Vega20c</option>
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290 <option value="gist_yarg">gist_yarg</option>
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291 <option value="tab10">tab10</option>
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292 <option value="coolwarm">coolwarm</option>
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293 <option value="winter_r">winter_r</option>
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294 <option value="plasma_r">plasma_r</option>
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295 <option value="Wistia">Wistia</option>
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296 <option value="BuGn_r">BuGn_r</option>
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297 <option value="Set2">Set2</option>
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298 <option value="Vega20_r">Vega20_r</option>
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299 <option value="hot">hot</option>
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300 <option value="brg">brg</option>
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301 <option value="BrBG_r">BrBG_r</option>
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302 <option value="gist_heat">gist_heat</option>
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303 <option value="YlOrRd">YlOrRd</option>
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304 <option value="inferno_r">inferno_r</option>
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305 <option value="viridis_r">viridis_r</option>
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306 <option value="gist_stern_r">gist_stern_r</option>
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307 <option value="tab20c_r">tab20c_r</option>
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308 <option value="gist_gray">gist_gray</option>
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309 <option value="Reds_r">Reds_r</option>
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310 <option value="flag_r">flag_r</option>
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311 <option value="Purples_r">Purples_r</option>
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312 <option value="vlag_r">vlag_r</option>
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313 <option value="summer_r">summer_r</option>
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314 <option value="Greys_r">Greys_r</option>
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315 <option value="PRGn">PRGn</option>
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316 <option value="PiYG">PiYG</option>
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317 <option value="gist_ncar">gist_ncar</option>
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318 <option value="Oranges">Oranges</option>
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319 <option value="Reds">Reds</option>
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320 <option value="GnBu_r">GnBu_r</option>
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321 <option value="RdPu">RdPu</option>
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322 <option value="YlOrBr_r">YlOrBr_r</option>
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323 <option value="autumn_r">autumn_r</option>
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324 <option value="YlGn">YlGn</option>
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325 <option value="CMRmap">CMRmap</option>
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326 <option value="gnuplot">gnuplot</option>
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327 <option value="rainbow_r">rainbow_r</option>
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328 <option value="PiYG_r">PiYG_r</option>
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329 <option value="Greens">Greens</option>
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330 <option value="YlOrBr">YlOrBr</option>
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331 <option value="prism_r">prism_r</option>
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332 <option value="winter">winter</option>
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333 <option value="gist_yarg_r">gist_yarg_r</option>
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334 <option value="Set2_r">Set2_r</option>
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335 <option value="nipy_spectral">nipy_spectral</option>
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336 <option value="plasma">plasma</option>
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337 <option value="OrRd">OrRd</option>
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338 <option value="Greens_r">Greens_r</option>
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339 <option value="tab10_r">tab10_r</option>
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340 <option value="YlGnBu">YlGnBu</option>
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341 <option value="prism">prism</option>
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342 <option value="PRGn_r">PRGn_r</option>
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343 <option value="gist_heat_r">gist_heat_r</option>
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344 <option value="terrain_r">terrain_r</option>
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345 <option value="tab20b">tab20b</option>
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346 <option value="PuBuGn">PuBuGn</option>
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347 <option value="PuBu_r">PuBu_r</option>
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348 <option value="spring_r">spring_r</option>
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349 <option value="gist_rainbow">gist_rainbow</option>
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350 <option value="cool">cool</option>
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351 <option value="PuOr">PuOr</option>
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352 <option value="PuRd_r">PuRd_r</option>
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353 <option value="gist_stern">gist_stern</option>
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354 <option value="PuBuGn_r">PuBuGn_r</option>
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355 </param>
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356 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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357
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358 </inputs>
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359
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360 <outputs>
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361 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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362
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363 </outputs>
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364
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365 <help><![CDATA[
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366 Generate a heatmap representation of a feature table
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367 ###############################################################
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368
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369 Generate a heatmap representation of a feature table with optional
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370 clustering on both the sample and feature axes. Tip: To generate a heatmap
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371 containing taxonomic annotations, use `qiime taxa collapse` to collapse the
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372 feature table at the desired taxonomic level.
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373
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374 Parameters
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375 ----------
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376 table : FeatureTable[Frequency]
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377 The feature table to visualize.
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378 sample_metadata : MetadataColumn[Categorical], optional
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379 Annotate the sample IDs with these sample metadata values. When
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380 metadata is present and `cluster`='feature', samples will be sorted by
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381 the metadata values.
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382 feature_metadata : MetadataColumn[Categorical], optional
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383 Annotate the feature IDs with these feature metadata values. When
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384 metadata is present and `cluster`='sample', features will be sorted by
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385 the metadata values.
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386 normalize : Bool, optional
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387 Normalize the feature table by adding a psuedocount of 1 and then
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388 taking the log10 of the table.
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389 title : Str, optional
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390 Optional custom plot title.
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391 metric : Str % Choices('yule', 'seuclidean', 'sokalmichener', 'sokalsneath', 'hamming', 'canberra', 'cityblock', 'russellrao', 'jaccard', 'braycurtis', 'minkowski', 'euclidean', 'kulsinski', 'cosine', 'sqeuclidean', 'correlation', 'dice', 'rogerstanimoto', 'mahalanobis', 'chebyshev', 'matching'), optional
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392 Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea
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393 born.clustermap.html#seaborn.clustermap for more detail).
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394 method : Str % Choices('complete', 'average', 'ward', 'median', 'weighted', 'centroid', 'single'), optional
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395 Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge
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396 nerated/seaborn.clustermap.html#seaborn.clustermap for more detail).
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397 cluster : Str % Choices('both', 'features', 'none', 'samples'), optional
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398 Specify which axes to cluster.
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399 color_scheme : Str % Choices('YlGn', 'flag', 'Greens_r', 'RdPu_r', 'OrRd', 'Set1_r', 'RdYlGn', 'inferno_r', 'Accent_r', 'bwr', 'PuOr', 'seismic_r', 'RdGy_r', 'tab20b_r', 'Oranges', 'spectral', 'RdYlGn_r', 'nipy_spectral_r', 'gist_gray', 'binary', 'gist_yarg_r', 'cubehelix', 'viridis_r', 'autumn', 'bone_r', 'terrain_r', 'RdPu', 'inferno', 'PRGn', 'YlGnBu', 'mako', 'gray', 'tab20_r', 'Oranges_r', 'gist_stern_r', 'Dark2_r', 'Purples_r', 'coolwarm', 'RdYlBu', 'tab10', 'copper_r', 'YlOrRd_r', 'gray_r', 'magma', 'Set3_r', 'BuGn', 'viridis', 'icefire_r', 'PuOr_r', 'YlOrBr', 'winter_r', 'hsv', 'gist_earth_r', 'rocket_r', 'Vega20b', 'autumn_r', 'gnuplot', 'Paired', 'PuRd_r', 'BrBG_r', 'plasma_r', 'Set2', 'prism', 'winter', 'seismic', 'RdGy', 'Blues_r', 'Reds_r', 'gist_ncar_r', 'Reds', 'afmhot', 'Greys', 'rainbow', 'tab10_r', 'GnBu_r', 'gnuplot2', 'pink', 'tab20b', 'BuGn_r', 'PuRd', 'gist_stern', 'magma_r', 'prism_r', 'tab20c_r', 'BuPu', 'cividis_r', 'BrBG', 'Wistia_r', 'gist_gray_r', 'ocean_r', 'summer_r', 'mako_r', 'CMRmap_r', 'cool_r', 'coolwarm_r', 'Greens', 'RdBu', 'icefire', 'spectral_r', 'Vega20', 'brg', 'Paired_r', 'BuPu_r', 'gist_rainbow', 'CMRmap', 'cool', 'gist_earth', 'bwr_r', 'rocket', 'YlGn_r', 'Vega20b_r', 'Wistia', 'Vega20c_r', 'Accent', 'plasma', 'Set1', 'PuBu_r', 'Purples', 'RdYlBu_r', 'brg_r', 'flag_r', 'Set3', 'hot_r', 'Blues', 'Pastel1_r', 'YlOrBr_r', 'hsv_r', 'Pastel2', 'Pastel1', 'bone', 'tab20', 'PuBuGn_r', 'terrain', 'gist_rainbow_r', 'Spectral_r', 'Pastel2_r', 'RdBu_r', 'summer', 'gist_ncar', 'OrRd_r', 'copper', 'tab20c', 'PuBuGn', 'Set2_r', 'vlag', 'jet_r', 'gist_heat_r', 'PRGn_r', 'Vega10', 'jet', 'Spectral', 'rainbow_r', 'binary_r', 'ocean', 'spring', 'Dark2', 'Vega20_r', 'vlag_r', 'PiYG', 'PuBu', 'YlGnBu_r', 'afmhot_r', 'nipy_spectral', 'gnuplot2_r', 'cividis', 'gnuplot_r', 'Greys_r', 'cubehelix_r', 'spring_r', 'PiYG_r', 'gist_yarg', 'gist_heat', 'Vega20c', 'GnBu', 'YlOrRd', 'hot', 'Vega10_r', 'pink_r'), optional
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400 The matplotlib colorscheme to generate the heatmap with.
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401
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402 Returns
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403 -------
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404 visualization : Visualization
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405 ]]></help>
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406 <macros>
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407 <import>qiime_citation.xml</import>
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408 </macros>
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409 <expand macro="qiime_citation"/>
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410 </tool> |
