annotate qiime2-2020.8/qiime_gneiss_dendrogram-heatmap.xml @ 25:499916460746 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:56:26 +0000
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1 <?xml version="1.0" ?>
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2 <tool id="qiime_gneiss_dendrogram-heatmap" name="qiime gneiss dendrogram-heatmap"
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3 version="2020.8">
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4 <description>Dendrogram heatmap.</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 gneiss dendrogram-heatmap
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10
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11 --i-table=$itable
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12
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13 --i-tree=$itree
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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($input_files_mmetadatafile)
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23 # end if
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24
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25 #if '__ob__' in str($mmetadatacolumn):
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26 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__ob__', '[')
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27 #set $mmetadatacolumn = $mmetadatacolumn_temp
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28 #end if
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29 #if '__cb__' in str($mmetadatacolumn):
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30 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__cb__', ']')
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31 #set $mmetadatacolumn = $mmetadatacolumn_temp
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32 #end if
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33 #if 'X' in str($mmetadatacolumn):
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34 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('X', '\\')
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35 #set $mmetadatacolumn = $mmetadatacolumn_temp
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36 #end if
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37 #if '__sq__' in str($mmetadatacolumn):
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38 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__sq__', "'")
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39 #set $mmetadatacolumn = $mmetadatacolumn_temp
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40 #end if
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41 #if '__db__' in str($mmetadatacolumn):
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42 #set $mmetadatacolumn_temp = $mmetadatacolumn.replace('__db__', '"')
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43 #set $mmetadatacolumn = $mmetadatacolumn_temp
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44 #end if
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45
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46 --m-metadata-column=$mmetadatacolumn
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47
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48
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49 --p-pseudocount=$ppseudocount
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50
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51 --p-ndim=$pndim
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52
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53 #if str($pmethod) != 'None':
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54 --p-method=$pmethod
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55 #end if
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56
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57 #if str($pcolormap) != 'None':
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58 --p-color-map=$pcolormap
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59 #end if
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60
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61 --o-visualization=ovisualization
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62
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63 #if str($examples) != 'None':
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64 --examples=$examples
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65 #end if
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66
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67 ;
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68 cp oclustering.qza $oclustering
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69
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70 ;
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71 qiime tools export ovisualization.qzv --output-path out
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72 && mkdir -p '$ovisualization.files_path'
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73 && cp -r out/* '$ovisualization.files_path'
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74 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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75
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76 ]]></command>
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77 <inputs>
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78 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] The feature table that will be plotted as a heatmap. This table is assumed to have strictly positive values. [required]" name="itable" optional="False" type="data" />
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79 <param format="qza,no_unzip.zip" label="--i-tree: ARTIFACT A hierarchy of feature identifiers where each Hierarchy tipcorresponds to the feature identifiers in the table. This tree can contain tip ids that are not present in the table, but all feature ids in the table must be present in this tree. [required]" name="itree" optional="False" type="data" />
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80 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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81 <param format="tabular,qza,no_unzip.zip" label="--m-metadata-file: METADATA" name="additional_input" optional="True" type="data" />
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82 </repeat>
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83 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Categorical metadata column to group the samples. [required]" name="mmetadatacolumn" optional="False" type="text" />
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84 <param label="--p-pseudocount: NUMBER The pseudocount to add to avoid division by zero. [default: 0.5]" name="ppseudocount" optional="True" type="float" value="0.5" />
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85 <param label="--p-ndim: INTEGER Number of dimensions to highlight. [default: 10]" name="pndim" optional="True" type="integer" value="10" />
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86 <param label="--p-method: " name="pmethod" optional="True" type="select">
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87 <option selected="True" value="None">Selection is Optional</option>
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88 <option value="clr">clr</option>
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89 <option value="log">log</option>
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90 </param>
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91 <param label="--p-color-map: " name="pcolormap" optional="True" type="select">
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92 <option selected="True" value="None">Selection is Optional</option>
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93 <option value="viridis">viridis</option>
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94 <option value="inferno">inferno</option>
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95 <option value="plasma">plasma</option>
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96 <option value="magma">magma</option>
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97 <option value="Blues">Blues</option>
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98 <option value="BuGn">BuGn</option>
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99 <option value="BuPu">BuPu</option>
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100 <option value="GnBu">GnBu</option>
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101 <option value="Greens">Greens</option>
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102 <option value="Greys">Greys</option>
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103 <option value="Oranges">Oranges</option>
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104 <option value="OrRd">OrRd</option>
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105 <option value="PuBu">PuBu</option>
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106 <option value="PuBuGn">PuBuGn</option>
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107 <option value="PuRd">PuRd</option>
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108 <option value="Purples">Purples</option>
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109 <option value="RdPu">RdPu</option>
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110 <option value="Reds">Reds</option>
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111 <option value="YlGn">YlGn</option>
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112 <option value="YlGnBu">YlGnBu</option>
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113 <option value="YlOrBr">YlOrBr</option>
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114 <option value="YlOrRd">YlOrRd</option>
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115 <option value="afmhot">afmhot</option>
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116 <option value="autumn">autumn</option>
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117 <option value="bone">bone</option>
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118 <option value="cool">cool</option>
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119 <option value="copper">copper</option>
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120 <option value="gist_heat">gist_heat</option>
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121 <option value="gray">gray</option>
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122 <option value="hot">hot</option>
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123 <option value="pink">pink</option>
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124 <option value="spring">spring</option>
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125 <option value="summer">summer</option>
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126 <option value="winter">winter</option>
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127 <option value="BrBG">BrBG</option>
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128 <option value="bwr">bwr</option>
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129 <option value="coolwarm">coolwarm</option>
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130 <option value="PiYG">PiYG</option>
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131 <option value="PRGn">PRGn</option>
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132 <option value="PuOr">PuOr</option>
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133 <option value="RdBu">RdBu</option>
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134 <option value="RdGy">RdGy</option>
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135 <option value="RdYlBu">RdYlBu</option>
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136 <option value="RdYlGn">RdYlGn</option>
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137 <option value="Spectral">Spectral</option>
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138 <option value="seismic">seismic</option>
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139 <option value="Accent">Accent</option>
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140 <option value="Dark2">Dark2</option>
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141 <option value="Paired">Paired</option>
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142 <option value="Pastel1">Pastel1</option>
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143 <option value="Pastel2">Pastel2</option>
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144 <option value="Set1">Set1</option>
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145 <option value="Set2">Set2</option>
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146 <option value="Set3">Set3</option>
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147 <option value="Vega10">Vega10</option>
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148 <option value="Vega20">Vega20</option>
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149 <option value="Vega20b">Vega20b</option>
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150 <option value="Vega20c">Vega20c</option>
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151 <option value="gist_earth">gist_earth</option>
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152 <option value="terrain">terrain</option>
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153 <option value="ocean">ocean</option>
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154 <option value="gist_stern">gist_stern</option>
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155 <option value="brg">brg</option>
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156 <option value="CMRmap">CMRmap</option>
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157 <option value="cubehelix">cubehelix</option>
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158 <option value="gnuplot">gnuplot</option>
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159 <option value="gnuplot2">gnuplot2</option>
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160 <option value="gist_ncar">gist_ncar</option>
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161 <option value="nipy_spectral">nipy_spectral</option>
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162 <option value="jet">jet</option>
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163 <option value="rainbow">rainbow</option>
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164 <option value="gist_rainbow">gist_rainbow</option>
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165 <option value="hsv">hsv</option>
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166 <option value="flag">flag</option>
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167 <option value="prism">prism</option>
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168 </param>
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169 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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170
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171 </inputs>
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172
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173 <outputs>
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174 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
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175
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176 </outputs>
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177
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178 <help><![CDATA[
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179 Dendrogram heatmap.
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180 ###############################################################
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181
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182 .. deprecated::
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183 This Visualizer is deprecated and will be removed in a future version of
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184 this plugin.
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185
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186 Visualize the feature table as a heatmap, with samples sorted along a
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187 specified categorical metadata column and features clustered together
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188 specified by the tree.
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189
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190 Parameters
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191 ----------
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192 table : FeatureTable[Frequency]
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193 The feature table that will be plotted as a heatmap. This table is
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194 assumed to have strictly positive values.
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195 tree : Hierarchy
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196 A hierarchy of feature identifiers where each tipcorresponds to the
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197 feature identifiers in the table. This tree can contain tip ids that
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198 are not present in the table, but all feature ids in the table must be
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199 present in this tree.
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200 metadata : MetadataColumn[Categorical]
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201 Categorical metadata column to group the samples.
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202 pseudocount : Float, optional
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203 The pseudocount to add to avoid division by zero.
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204 ndim : Int, optional
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205 Number of dimensions to highlight.
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206 method : Str % Choices('clr', 'log'), optional
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207 Specifies how the data should be normalized for display.Options include
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208 'log' or 'clr' (default='clr').
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209 color_map : Str % Choices('viridis', 'inferno', 'plasma', 'magma', 'Blues', 'BuGn', 'BuPu', 'GnBu', 'Greens', 'Greys', 'Oranges', 'OrRd', 'PuBu', 'PuBuGn', 'PuRd', 'Purples', 'RdPu', 'Reds', 'YlGn', 'YlGnBu', 'YlOrBr', 'YlOrRd', 'afmhot', 'autumn', 'bone', 'cool', 'copper', 'gist_heat', 'gray', 'hot', 'pink', 'spring', 'summer', 'winter', 'BrBG', 'bwr', 'coolwarm', 'PiYG', 'PRGn', 'PuOr', 'RdBu', 'RdGy', 'RdYlBu', 'RdYlGn', 'Spectral', 'seismic', 'Accent', 'Dark2', 'Paired', 'Pastel1', 'Pastel2', 'Set1', 'Set2', 'Set3', 'Vega10', 'Vega20', 'Vega20b', 'Vega20c', 'gist_earth', 'terrain', 'ocean', 'gist_stern', 'brg', 'CMRmap', 'cubehelix', 'gnuplot', 'gnuplot2', 'gist_ncar', 'nipy_spectral', 'jet', 'rainbow', 'gist_rainbow', 'hsv', 'flag', 'prism'), optional
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210 Specifies the color map for plotting the heatmap. See
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211 https://matplotlib.org/examples/color/colormaps_reference.html for more
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212 details.
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213
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214 Returns
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215 -------
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216 visualization : Visualization
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217 ]]></help>
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218 <macros>
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219 <import>qiime_citation.xml</import>
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220 </macros>
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221 <expand macro="qiime_citation"/>
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222 </tool>