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1 <?xml version="1.0" ?>
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2 <tool id="qiime_sample-classifier_heatmap" name="qiime sample-classifier heatmap" version="2019.4">
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3 <description> - Generate heatmap of important features.</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime sample-classifier heatmap
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9
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10 --i-table=$itable
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11 --i-importance=$iimportance
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12
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13
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14 #if $input_files_mmetadatafile:
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15 #def list_dict_to_string(list_dict):
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16 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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17 #for d in list_dict[1:]:
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18 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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19 #end for
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20 #return $file_list
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21 #end def
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22 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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23 #end if
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24
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25
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26
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27 #if str($mmetadatacolumn):
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28 --m-metadata-column="$mmetadatacolumn"
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29 #end if
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30
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31 #if $pfeaturecount:
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32 --p-feature-count=$pfeaturecount
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33 #end if
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34
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35 #if $pimportancethreshold:
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36 --p-importance-threshold=$pimportancethreshold
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37 #end if
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38
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39 #if $pgroupsamples:
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40 --p-group-samples
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41 #end if
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42
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43 #if $pnonormalize:
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44 --p-no-normalize
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45 #end if
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46
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47 #if str($pmetric) != 'None':
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48 --p-metric=$pmetric
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49 #end if
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50
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51 #if str($pmethod) != 'None':
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52 --p-method=$pmethod
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53 #end if
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54
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55 #if str($pcluster) != 'None':
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56 --p-cluster=$pcluster
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57 #end if
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58
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59 #if str($pcolorscheme) != 'None':
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60 --p-color-scheme=$pcolorscheme
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61 #end if
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62
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63 --o-heatmap=oheatmap
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64 --o-filtered-table=ofilteredtable
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65 ;
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66 qiime tools export --input-path oheatmap.qzv --output-path out && mkdir -p '$oheatmap.files_path'
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67 && cp -r out/* '$oheatmap.files_path'
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68 && mv '$oheatmap.files_path/index.html' '$oheatmap';
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69 cp ofilteredtable.qza $ofilteredtable
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70 ]]></command>
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71 <inputs>
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72 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table containing all features that should be used for target prediction. [required]" name="itable" optional="False" type="data"/>
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73 <param format="qza,no_unzip.zip" label="--i-importance: ARTIFACT FeatureData[Importance] Feature importances. [required]" name="iimportance" optional="False" type="data"/>
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74 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Metadata file to convert to feature table. [optional]" name="mmetadatacolumn" optional="True" type="text"/>
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75 <param label="--p-feature-count: INTEGER Range(0, None) Filter feature table to include top N most important features. Set to zero to include all features. [default: 50]" name="pfeaturecount" optional="True" type="integer" value="50" min="0"/>
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76 <param label="--p-importance-threshold: NUMBER Range(0, None) Filter feature table to exclude any features with an importance score less than this threshold. Set to zero to include all features. [default: 0]" name="pimportancethreshold" optional="True" type="float" value="0" min="0"/>
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77 <param label="--p-group-samples: --p-no-group-samples Group samples by metadata. [default: False]" name="pgroupsamples" selected="False" type="boolean"/>
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78 <param label="--p-no-normalize: Normalize the feature table by adding a psuedocount of 1 and then taking the log10 of the table. [default: False]" name="pnonormalize" selected="False" type="boolean"/>
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79 <param label="--p-metric: " name="pmetric" optional="True" type="select">
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80 <option selected="True" value="None">Selection is Optional</option>
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81 <option value="kulsinski">kulsinski</option>
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82 <option value="correlation">correlation</option>
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83 <option value="hamming">hamming</option>
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84 <option value="canberra">canberra</option>
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85 <option value="sqeuclidean">sqeuclidean</option>
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86 <option value="sokalmichener">sokalmichener</option>
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87 <option value="cityblock">cityblock</option>
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88 <option value="braycurtis">braycurtis</option>
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89 <option value="matching">matching</option>
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90 <option value="russellrao">russellrao</option>
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91 <option value="cosine">cosine</option>
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92 <option value="yule">yule</option>
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93 <option value="minkowski">minkowski</option>
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94 <option value="euclidean">euclidean</option>
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95 <option value="rogerstanimoto">rogerstanimoto</option>
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96 <option value="seuclidean">seuclidean</option>
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97 <option value="jaccard">jaccard</option>
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98 <option value="sokalsneath">sokalsneath</option>
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99 <option value="chebyshev">chebyshev</option>
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100 <option value="dice">dice</option>
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101 <option value="mahalanobis">mahalanobis</option>
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102 </param>
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103 <param label="--p-method: " name="pmethod" optional="True" type="select">
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104 <option selected="True" value="None">Selection is Optional</option>
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105 <option value="complete">complete</option>
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106 <option value="centroid">centroid</option>
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107 <option value="weighted">weighted</option>
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108 <option value="single">single</option>
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109 <option value="ward">ward</option>
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110 <option value="average">average</option>
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111 <option value="median">median</option>
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112 </param>
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113 <param label="--p-cluster: " name="pcluster" optional="True" type="select">
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114 <option selected="True" value="None">Selection is Optional</option>
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115 <option value="features">features</option>
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116 <option value="both">both</option>
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117 <option value="samples">samples</option>
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118 <option value="none">none</option>
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119 </param>
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120 <param label="--p-color-scheme: " name="pcolorscheme" optional="True" type="select">
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121 <option selected="True" value="None">Selection is Optional</option>
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122 <option value="bone">bone</option>
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123 <option value="PRGn_r">PRGn_r</option>
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124 <option value="Vega10_r">Vega10_r</option>
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125 <option value="GnBu">GnBu</option>
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126 <option value="hsv">hsv</option>
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127 <option value="binary_r">binary_r</option>
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128 <option value="GnBu_r">GnBu_r</option>
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129 <option value="icefire">icefire</option>
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130 <option value="winter">winter</option>
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131 <option value="BuGn_r">BuGn_r</option>
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132 <option value="plasma_r">plasma_r</option>
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133 <option value="Vega20_r">Vega20_r</option>
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134 <option value="summer_r">summer_r</option>
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135 <option value="cool_r">cool_r</option>
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136 <option value="Spectral">Spectral</option>
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137 <option value="gist_heat_r">gist_heat_r</option>
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138 <option value="Vega20b_r">Vega20b_r</option>
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139 <option value="mako_r">mako_r</option>
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140 <option value="RdBu_r">RdBu_r</option>
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141 <option value="cubehelix">cubehelix</option>
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142 <option value="tab20b_r">tab20b_r</option>
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143 <option value="CMRmap">CMRmap</option>
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144 <option value="Greys">Greys</option>
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145 <option value="PuOr">PuOr</option>
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146 <option value="cubehelix_r">cubehelix_r</option>
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147 <option value="Wistia">Wistia</option>
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148 <option value="gnuplot2">gnuplot2</option>
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149 <option value="bwr">bwr</option>
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150 <option value="gnuplot_r">gnuplot_r</option>
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151 <option value="viridis">viridis</option>
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152 <option value="gist_ncar_r">gist_ncar_r</option>
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153 <option value="gist_ncar">gist_ncar</option>
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154 <option value="plasma">plasma</option>
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155 <option value="PuRd">PuRd</option>
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156 <option value="afmhot">afmhot</option>
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157 <option value="icefire_r">icefire_r</option>
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158 <option value="tab20b">tab20b</option>
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159 <option value="gist_yarg_r">gist_yarg_r</option>
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160 <option value="hot">hot</option>
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161 <option value="YlOrRd_r">YlOrRd_r</option>
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162 <option value="Vega20c">Vega20c</option>
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163 <option value="Dark2_r">Dark2_r</option>
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164 <option value="Set3">Set3</option>
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165 <option value="PuBu">PuBu</option>
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166 <option value="magma">magma</option>
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167 <option value="Pastel2">Pastel2</option>
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168 <option value="terrain">terrain</option>
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169 <option value="autumn_r">autumn_r</option>
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170 <option value="spectral">spectral</option>
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171 <option value="brg">brg</option>
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172 <option value="Set3_r">Set3_r</option>
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173 <option value="coolwarm">coolwarm</option>
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174 <option value="Set2_r">Set2_r</option>
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175 <option value="Paired_r">Paired_r</option>
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176 <option value="tab20c_r">tab20c_r</option>
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177 <option value="mako">mako</option>
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178 <option value="gist_rainbow_r">gist_rainbow_r</option>
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179 <option value="RdBu">RdBu</option>
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180 <option value="PuBu_r">PuBu_r</option>
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181 <option value="jet_r">jet_r</option>
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182 <option value="gist_earth_r">gist_earth_r</option>
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183 <option value="Greys_r">Greys_r</option>
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184 <option value="gray">gray</option>
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185 <option value="winter_r">winter_r</option>
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186 <option value="rocket">rocket</option>
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187 <option value="Set2">Set2</option>
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188 <option value="seismic_r">seismic_r</option>
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189 <option value="Pastel1">Pastel1</option>
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190 <option value="RdYlGn_r">RdYlGn_r</option>
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191 <option value="copper">copper</option>
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192 <option value="spring_r">spring_r</option>
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193 <option value="BuGn">BuGn</option>
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194 <option value="Greens">Greens</option>
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195 <option value="Blues">Blues</option>
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196 <option value="PiYG_r">PiYG_r</option>
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197 <option value="YlGnBu">YlGnBu</option>
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198 <option value="Paired">Paired</option>
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199 <option value="YlGn_r">YlGn_r</option>
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200 <option value="RdPu_r">RdPu_r</option>
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201 <option value="BrBG_r">BrBG_r</option>
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202 <option value="bone_r">bone_r</option>
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203 <option value="RdYlBu">RdYlBu</option>
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204 <option value="gist_rainbow">gist_rainbow</option>
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205 <option value="bwr_r">bwr_r</option>
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206 <option value="inferno_r">inferno_r</option>
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207 <option value="inferno">inferno</option>
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208 <option value="gist_stern_r">gist_stern_r</option>
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209 <option value="gray_r">gray_r</option>
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210 <option value="Purples">Purples</option>
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211 <option value="RdGy">RdGy</option>
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212 <option value="hot_r">hot_r</option>
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213 <option value="YlOrBr_r">YlOrBr_r</option>
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214 <option value="nipy_spectral">nipy_spectral</option>
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215 <option value="nipy_spectral_r">nipy_spectral_r</option>
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216 <option value="ocean">ocean</option>
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217 <option value="Set1">Set1</option>
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218 <option value="Dark2">Dark2</option>
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219 <option value="Oranges">Oranges</option>
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220 <option value="Pastel1_r">Pastel1_r</option>
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221 <option value="Oranges_r">Oranges_r</option>
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222 <option value="Pastel2_r">Pastel2_r</option>
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223 <option value="YlGn">YlGn</option>
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224 <option value="Vega20b">Vega20b</option>
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225 <option value="PuRd_r">PuRd_r</option>
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226 <option value="PuBuGn_r">PuBuGn_r</option>
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227 <option value="afmhot_r">afmhot_r</option>
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228 <option value="spring">spring</option>
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229 <option value="tab20_r">tab20_r</option>
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230 <option value="PuBuGn">PuBuGn</option>
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231 <option value="gist_yarg">gist_yarg</option>
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232 <option value="PiYG">PiYG</option>
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233 <option value="flag">flag</option>
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234 <option value="rainbow_r">rainbow_r</option>
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235 <option value="hsv_r">hsv_r</option>
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236 <option value="prism_r">prism_r</option>
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237 <option value="ocean_r">ocean_r</option>
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238 <option value="magma_r">magma_r</option>
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239 <option value="flag_r">flag_r</option>
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240 <option value="Blues_r">Blues_r</option>
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241 <option value="gnuplot2_r">gnuplot2_r</option>
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242 <option value="gist_gray">gist_gray</option>
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243 <option value="spectral_r">spectral_r</option>
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244 <option value="CMRmap_r">CMRmap_r</option>
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245 <option value="rainbow">rainbow</option>
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246 <option value="gnuplot">gnuplot</option>
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247 <option value="vlag">vlag</option>
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248 <option value="Set1_r">Set1_r</option>
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249 <option value="Accent">Accent</option>
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250 <option value="coolwarm_r">coolwarm_r</option>
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251 <option value="brg_r">brg_r</option>
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252 <option value="pink_r">pink_r</option>
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253 <option value="YlOrBr">YlOrBr</option>
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254 <option value="Vega20c_r">Vega20c_r</option>
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255 <option value="Wistia_r">Wistia_r</option>
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256 <option value="RdGy_r">RdGy_r</option>
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257 <option value="tab20">tab20</option>
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258 <option value="BrBG">BrBG</option>
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259 <option value="rocket_r">rocket_r</option>
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260 <option value="OrRd_r">OrRd_r</option>
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261 <option value="YlGnBu_r">YlGnBu_r</option>
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262 <option value="viridis_r">viridis_r</option>
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263 <option value="copper_r">copper_r</option>
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264 <option value="gist_heat">gist_heat</option>
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265 <option value="Vega10">Vega10</option>
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266 <option value="PuOr_r">PuOr_r</option>
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267 <option value="binary">binary</option>
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268 <option value="pink">pink</option>
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269 <option value="Reds">Reds</option>
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270 <option value="Purples_r">Purples_r</option>
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271 <option value="cool">cool</option>
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272 <option value="prism">prism</option>
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273 <option value="terrain_r">terrain_r</option>
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274 <option value="BuPu_r">BuPu_r</option>
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275 <option value="Spectral_r">Spectral_r</option>
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276 <option value="Greens_r">Greens_r</option>
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277 <option value="gist_gray_r">gist_gray_r</option>
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278 <option value="RdYlGn">RdYlGn</option>
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279 <option value="tab20c">tab20c</option>
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280 <option value="Reds_r">Reds_r</option>
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281 <option value="tab10">tab10</option>
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282 <option value="summer">summer</option>
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283 <option value="gist_stern">gist_stern</option>
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284 <option value="tab10_r">tab10_r</option>
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285 <option value="YlOrRd">YlOrRd</option>
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286 <option value="jet">jet</option>
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287 <option value="Vega20">Vega20</option>
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288 <option value="vlag_r">vlag_r</option>
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289 <option value="RdPu">RdPu</option>
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290 <option value="OrRd">OrRd</option>
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291 <option value="Accent_r">Accent_r</option>
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292 <option value="autumn">autumn</option>
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293 <option value="BuPu">BuPu</option>
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294 <option value="RdYlBu_r">RdYlBu_r</option>
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295 <option value="gist_earth">gist_earth</option>
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296 <option value="seismic">seismic</option>
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297 <option value="PRGn">PRGn</option>
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298 </param>
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299
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300 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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301 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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302 </repeat>
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303
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304 </inputs>
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305 <outputs>
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306 <data format="html" label="${tool.name} on ${on_string}: heatmap.qzv" name="oheatmap"/>
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307 <data format="qza" label="${tool.name} on ${on_string}: filteredtable.qza" name="ofilteredtable"/>
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308 </outputs>
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309 <help><![CDATA[
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310 Generate heatmap of important features.
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311 #######################################
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312
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313 Generate a heatmap of important features. Features are filtered based on
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314 importance scores; samples are optionally grouped by metadata; and a
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315 heatmap is generated that displays (normalized) feature abundances per
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316 sample.
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317
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318 Parameters
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319 ----------
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320 table : FeatureTable[Frequency]
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321 Feature table containing all features that should be used for target
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322 prediction.
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323 importance : FeatureData[Importance]
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324 Feature importances.
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325 metadata : MetadataColumn[Categorical], optional
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326 Metadata file to convert to feature table.
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327 feature_count : Int % Range(0, None), optional
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328 Filter feature table to include top N most important features. Set to
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329 zero to include all features.
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330 importance_threshold : Float % Range(0, None), optional
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331 Filter feature table to exclude any features with an importance score
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332 less than this threshold. Set to zero to include all features.
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333 group_samples : Bool, optional
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334 Group samples by metadata.
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335 normalize : Bool, optional
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336 Normalize the feature table by adding a psuedocount of 1 and then
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337 taking the log10 of the table.
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338 metric : Str % Choices('sokalmichener', 'yule', 'russellrao', 'rogerstanimoto', 'minkowski', 'correlation', 'jaccard', 'cosine', 'chebyshev', 'euclidean', 'sqeuclidean', 'cityblock', 'matching', 'dice', 'mahalanobis', 'kulsinski', 'seuclidean', 'sokalsneath', 'canberra', 'hamming', 'braycurtis'), optional
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339 Metrics exposed by seaborn (see http://seaborn.pydata.org/generated/sea
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340 born.clustermap.html#seaborn.clustermap for more detail).
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341 method : Str % Choices('average', 'complete', 'median', 'centroid', 'single', 'ward', 'weighted'), optional
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342 Clustering methods exposed by seaborn (see http://seaborn.pydata.org/ge
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343 nerated/seaborn.clustermap.html#seaborn.clustermap for more detail).
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344 cluster : Str % Choices('features', 'samples', 'none', 'both'), optional
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345 Specify which axes to cluster.
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346 color_scheme : Str % Choices('rocket', 'RdYlBu_r', 'winter', 'viridis', 'BrBG', 'magma_r', 'YlOrBr', 'seismic', 'Set1', 'gist_yarg_r', 'gist_rainbow', 'autumn_r', 'Wistia_r', 'cool_r', 'hsv_r', 'flag', 'Vega20b_r', 'mako_r', 'coolwarm', 'Vega20_r', 'jet', 'cubehelix_r', 'bwr_r', 'brg', 'RdPu', 'gist_ncar', 'RdPu_r', 'cool', 'gnuplot_r', 'Set3', 'ocean_r', 'tab20b', 'tab20b_r', 'OrRd_r', 'Spectral_r', 'gray', 'OrRd', 'prism_r', 'Wistia', 'hot', 'icefire', 'plasma', 'Purples_r', 'viridis_r', 'gnuplot2_r', 'CMRmap', 'YlGnBu_r', 'Set3_r', 'PuRd_r', 'Reds_r', 'gray_r', 'Dark2', 'Vega20b', 'Paired', 'gist_yarg', 'RdYlGn_r', 'Greens', 'YlGnBu', 'tab20', 'gnuplot', 'PuBuGn_r', 'spectral_r', 'tab20c_r', 'gist_rainbow_r', 'hot_r', 'spring_r', 'gist_gray', 'Blues_r', 'Spectral', 'magma', 'GnBu_r', 'inferno_r', 'tab10', 'gist_gray_r', 'seismic_r', 'spring', 'BuPu_r', 'spectral', 'BrBG_r', 'PiYG', 'inferno', 'YlOrBr_r', 'Set1_r', 'YlOrRd_r', 'summer', 'vlag', 'Oranges_r', 'Dark2_r', 'binary_r', 'icefire_r', 'RdYlGn', 'hsv', 'gist_heat', 'PRGn_r', 'pink_r', 'Pastel2_r', 'copper_r', 'BuGn', 'gist_stern_r', 'PuRd', 'gist_earth_r', 'YlOrRd', 'Reds', 'gist_earth', 'Greens_r', 'Vega10', 'ocean', 'brg_r', 'rainbow_r', 'tab20_r', 'Purples', 'Blues', 'Accent', 'afmhot_r', 'Set2_r', 'RdBu', 'Vega20c', 'Pastel1', 'RdGy_r', 'PuBuGn', 'copper', 'PuOr', 'jet_r', 'YlGn_r', 'gist_heat_r', 'PuOr_r', 'bone', 'BuGn_r', 'terrain_r', 'mako', 'Vega20c_r', 'Paired_r', 'PuBu_r', 'tab20c', 'Pastel1_r', 'flag_r', 'plasma_r', 'Oranges', 'autumn', 'bone_r', 'GnBu', 'bwr', 'Greys', 'RdBu_r', 'RdGy', 'winter_r', 'gnuplot2', 'coolwarm_r', 'pink', 'nipy_spectral', 'Greys_r', 'summer_r', 'Vega20', 'BuPu', 'afmhot', 'gist_stern', 'binary', 'PiYG_r', 'YlGn', 'rocket_r', 'cubehelix', 'rainbow', 'Accent_r', 'CMRmap_r', 'PRGn', 'PuBu', 'tab10_r', 'prism', 'vlag_r', 'Set2', 'gist_ncar_r', 'nipy_spectral_r', 'Pastel2', 'terrain', 'RdYlBu', 'Vega10_r'), optional
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347 Color scheme for heatmap.
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348
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349 Returns
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350 -------
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351 heatmap : Visualization
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352 Heatmap of important features.
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353 filtered_table : FeatureTable[Frequency]
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354 Filtered feature table containing data displayed in heatmap.
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355 ]]></help>
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356 <macros>
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357 <import>qiime_citation.xml</import>
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358 </macros>
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359 <expand macro="qiime_citation"/>
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360 </tool>
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