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1 <?xml version="1.0" ?>
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2 <tool id="qiime_diversity_core-metrics-phylogenetic" name="qiime diversity core-metrics-phylogenetic" version="2018.4">
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3 <description> - Core diversity metrics (phylogenetic and non- phylogenetic)</description>
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4 <requirements>
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5 <requirement type="package" version="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime diversity core-metrics-phylogenetic --i-table=$itable
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9
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10 #def list_dict_to_string(list_dict):
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11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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12 #for d in list_dict[1:]:
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13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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14 #end for
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15 #return $file_list
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16 #end def
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17
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18 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile) --i-phylogeny=$iphylogeny --p-sampling-depth="$psamplingdepth"
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19
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20 #if str($cmdconfig) != 'None':
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21 --cmd-config=$cmdconfig
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22 #end if
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23
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24 --o-unweighted-unifrac-emperor=ounweightedunifracemperor --o-weighted-unifrac-distance-matrix=oweightedunifracdistancematrix --o-unweighted-unifrac-distance-matrix=ounweightedunifracdistancematrix --o-bray-curtis-pcoa-results=obraycurtispcoaresults --o-observed-otus-vector=oobservedotusvector --o-faith-pd-vector=ofaithpdvector --o-jaccard-pcoa-results=ojaccardpcoaresults --o-weighted-unifrac-pcoa-results=oweightedunifracpcoaresults --o-jaccard-emperor=ojaccardemperor --o-shannon-vector=oshannonvector --o-bray-curtis-distance-matrix=obraycurtisdistancematrix --o-bray-curtis-emperor=obraycurtisemperor --o-rarefied-table=orarefiedtable --o-jaccard-distance-matrix=ojaccarddistancematrix
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25
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26 #set $pnjobs = '${GALAXY_SLOTS:-4}'
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27
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28 #if str($pnjobs):
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29 --p-n-jobs="$pnjobs"
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30 #end if
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31
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32 --o-weighted-unifrac-emperor=oweightedunifracemperor --o-evenness-vector=oevennessvector --o-unweighted-unifrac-pcoa-results=ounweightedunifracpcoaresults;
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33
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34
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35 qiime tools export ounweightedunifracemperor.qzv --output-dir out && mkdir -p '$ounweightedunifracemperor.files_path'
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36 && cp -r out/* '$ounweightedunifracemperor.files_path'
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37 && mv '$ounweightedunifracemperor.files_path/index.html' '$ounweightedunifracemperor';
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38
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39 cp oweightedunifracdistancematrix.qza $oweightedunifracdistancematrix;
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40 cp ounweightedunifracdistancematrix.qza $ounweightedunifracdistancematrix;
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41 cp obraycurtispcoaresults.qza $obraycurtispcoaresults;
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42 cp oobservedotusvector.qza $oobservedotusvector;
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43 cp ofaithpdvector.qza $ofaithpdvector;
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44 cp ojaccardpcoaresults.qza $ojaccardpcoaresults;
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45 cp oweightedunifracpcoaresults.qza $oweightedunifracpcoaresults;
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46
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47
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48 qiime tools export ojaccardemperor.qzv --output-dir out && mkdir -p '$ojaccardemperor.files_path'
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49 && cp -r out/* '$ojaccardemperor.files_path'
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50 && mv '$ojaccardemperor.files_path/index.html' '$ojaccardemperor';
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51
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52 cp oshannonvector.qza $oshannonvector;
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53 cp obraycurtisdistancematrix.qza $obraycurtisdistancematrix;
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54
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55 qiime tools export obraycurtisemperor.qzv --output-dir out && mkdir -p '$obraycurtisemperor.files_path'
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56 && cp -r out/* '$obraycurtisemperor.files_path'
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57 && mv '$obraycurtisemperor.files_path/index.html' '$obraycurtisemperor';
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58
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59 cp orarefiedtable.qza $orarefiedtable;
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60 cp ojaccarddistancematrix.qza $ojaccarddistancematrix;
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61
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62 qiime tools export oweightedunifracemperor.qzv --output-dir out && mkdir -p '$oweightedunifracemperor.files_path'
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63 && cp -r out/* '$oweightedunifracemperor.files_path'
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64 && mv '$oweightedunifracemperor.files_path/index.html' '$oweightedunifracemperor';
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65
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66 cp oevennessvector.qza $oevennessvector;
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67 cp ounweightedunifracpcoaresults.qza $ounweightedunifracpcoaresults;
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68 ]]></command>
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69 <inputs>
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70 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] The feature table containing the samples over which diversity metrics should be computed. [required]" name="itable" optional="False" type="data"/>
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71 <param format="qza,no_unzip.zip" label="--i-phylogeny: Phylogeny[Rooted] Phylogenetic tree containing tip identifiers that correspond 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="iphylogeny" optional="False" type="data"/>
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72 <param label="--p-sampling-depth: The total frequency that each sample should be rarefied to prior to computing diversity metrics. [required]" name="psamplingdepth" optional="False" type="text"/>
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73 <repeat name="input_files_mmetadatafile" optional="False" title="--m-metadata-file">
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74 <param label="--m-metadata-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. The sample metadata to use in the emperor plots. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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75 </repeat>
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76 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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77 </inputs>
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78 <outputs>
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79 <data format="qza" label="${tool.name} on ${on_string}: rarefied-table.qza" name="orarefiedtable"/>
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80 <data format="qza" label="${tool.name} on ${on_string}: faith-pd-vector.qza" name="ofaithpdvector"/>
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81 <data format="qza" label="${tool.name} on ${on_string}: observed-otus-vector.qza" name="oobservedotusvector"/>
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82 <data format="qza" label="${tool.name} on ${on_string}: shannon-vector.qza" name="oshannonvector"/>
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83 <data format="qza" label="${tool.name} on ${on_string}: evenness-vector.qza" name="oevennessvector"/>
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84 <data format="qza" label="${tool.name} on ${on_string}: unweighted-unifrac-distance-matrix.qza" name="ounweightedunifracdistancematrix"/>
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85 <data format="qza" label="${tool.name} on ${on_string}: weighted-unifrac-distance-matrix.qza" name="oweightedunifracdistancematrix"/>
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86 <data format="qza" label="${tool.name} on ${on_string}: jaccard-distance-matrix.qza" name="ojaccarddistancematrix"/>
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87 <data format="qza" label="${tool.name} on ${on_string}: bray-curtis-distance-matrix.qza" name="obraycurtisdistancematrix"/>
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88 <data format="qza" label="${tool.name} on ${on_string}: unweighted-unifrac-pcoa-results.qza" name="ounweightedunifracpcoaresults"/>
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89 <data format="qza" label="${tool.name} on ${on_string}: weighted-unifrac-pcoa-results.qza" name="oweightedunifracpcoaresults"/>
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90 <data format="qza" label="${tool.name} on ${on_string}: jaccard-pcoa-results.qza" name="ojaccardpcoaresults"/>
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91 <data format="qza" label="${tool.name} on ${on_string}: bray-curtis-pcoa-results.qza" name="obraycurtispcoaresults"/>
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92 <data format="html" label="${tool.name} on ${on_string}: unweighted-unifrac-emperor.qzv" name="ounweightedunifracemperor"/>
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93 <data format="html" label="${tool.name} on ${on_string}: weighted-unifrac-emperor.qzv" name="oweightedunifracemperor"/>
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94 <data format="html" label="${tool.name} on ${on_string}: jaccard-emperor.qzv" name="ojaccardemperor"/>
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95 <data format="html" label="${tool.name} on ${on_string}: bray-curtis-emperor.qzv" name="obraycurtisemperor"/>
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96 </outputs>
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97 <help><![CDATA[
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98 Core diversity metrics (phylogenetic and non-phylogenetic)
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99 ----------------------------------------------------------
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100
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101 Applies a collection of diversity metrics (both phylogenetic and non-
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102 phylogenetic) to a feature table.
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103
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104 Parameters
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105 ----------
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106 table : FeatureTable[Frequency]
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107 The feature table containing the samples over which diversity metrics
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108 should be computed.
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109 phylogeny : Phylogeny[Rooted]
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110 Phylogenetic tree containing tip identifiers that correspond to the
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111 feature identifiers in the table. This tree can contain tip ids that
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112 are not present in the table, but all feature ids in the table must be
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113 present in this tree.
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114 sampling_depth : Int % Range(1, None)
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115 The total frequency that each sample should be rarefied to prior to
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116 computing diversity metrics.
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117 metadata : Metadata
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118 The sample metadata to use in the emperor plots.
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119
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120 Returns
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121 -------
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122 rarefied_table : FeatureTable[Frequency]
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123 The resulting rarefied feature table.
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124 faith_pd_vector : SampleData[AlphaDiversity]
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125 Vector of Faith PD values by sample.
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126 observed_otus_vector : SampleData[AlphaDiversity]
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127 Vector of Observed OTUs values by sample.
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128 shannon_vector : SampleData[AlphaDiversity]
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129 Vector of Shannon diversity values by sample.
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130 evenness_vector : SampleData[AlphaDiversity]
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131 Vector of Pielou's evenness values by sample.
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132 unweighted_unifrac_distance_matrix : DistanceMatrix
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133 Matrix of unweighted UniFrac distances between pairs of samples.
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134 weighted_unifrac_distance_matrix : DistanceMatrix
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135 Matrix of weighted UniFrac distances between pairs of samples.
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136 jaccard_distance_matrix : DistanceMatrix
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137 Matrix of Jaccard distances between pairs of samples.
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138 bray_curtis_distance_matrix : DistanceMatrix
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139 Matrix of Bray-Curtis distances between pairs of samples.
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140 unweighted_unifrac_pcoa_results : PCoAResults
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141 PCoA matrix computed from unweighted UniFrac distances between samples.
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142 weighted_unifrac_pcoa_results : PCoAResults
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143 PCoA matrix computed from weighted UniFrac distances between samples.
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144 jaccard_pcoa_results : PCoAResults
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145 PCoA matrix computed from Jaccard distances between samples.
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146 bray_curtis_pcoa_results : PCoAResults
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147 PCoA matrix computed from Bray-Curtis distances between samples.
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148 unweighted_unifrac_emperor : Visualization
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149 Emperor plot of the PCoA matrix computed from unweighted UniFrac.
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150 weighted_unifrac_emperor : Visualization
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151 Emperor plot of the PCoA matrix computed from weighted UniFrac.
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152 jaccard_emperor : Visualization
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153 Emperor plot of the PCoA matrix computed from Jaccard.
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154 bray_curtis_emperor : Visualization
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155 Emperor plot of the PCoA matrix computed from Bray-Curtis.
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156 ]]>
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157 </help>
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158 </tool>
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