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1 <?xml version="1.0" ?>
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2 <tool id="qiime_quality-control_evaluate-composition" name="qiime quality-control evaluate-composition" version="2019.4">
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3 <description> - Evaluate expected vs. observed taxonomic composition of samples</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 quality-control evaluate-composition
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9
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10 --i-expected-features=$iexpectedfeatures
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11 --i-observed-features=$iobservedfeatures
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12
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13 #if $input_files_mmetadatafile:
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14 #def list_dict_to_string(list_dict):
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15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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16 #for d in list_dict[1:]:
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17 #set $file_list = $file_list + ' --m-metadata-file=' + d['additional_input'].__getattr__('file_name')
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18 #end for
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19 #return $file_list
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20 #end def
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21 --m-metadata-file=$list_dict_to_string($input_files_mmetadatafile)
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22 #end if
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23
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24
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25 #if $pdepth:
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26 --p-depth=$pdepth
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27 #end if
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28
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29 #if str($ppalette) != 'None':
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30 --p-palette=$ppalette
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31 #end if
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32
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33 #if $pplottar:
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34 --p-plot-tar
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35 #end if
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36
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37 #if $pplottdr:
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38 --p-plot-tdr
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39 #end if
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40
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41 #if $pplotrvalue:
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42 --p-plot-r-value
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43 #end if
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44
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45 #if $pnoplotrsquared:
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46 --p-no-plot-r-squared
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47 #end if
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48
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49 #if $pplotbraycurtis:
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50 --p-plot-bray-curtis
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51 #end if
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52
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53 #if $pplotjaccard:
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54 --p-plot-jaccard
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55 #end if
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56
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57 #if $pplotobservedfeatures:
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58 --p-plot-observed-features
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59 #end if
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60
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61 #if $pplotobservedfeaturesratio:
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62 --p-plot-observed-features-ratio
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63 #end if
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64
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65 #if str($mmetadatacolumn):
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66 --m-metadata-column="$mmetadatacolumn"
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67 #end if
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68
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69 --o-visualization=ovisualization
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70 ;
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71 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
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72 && cp -r out/* '$ovisualization.files_path'
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73 && mv '$ovisualization.files_path/index.html' '$ovisualization'
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74 ]]></command>
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75 <inputs>
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76 <param format="qza,no_unzip.zip" label="--i-expected-features: ARTIFACT FeatureTable[RelativeFrequency] Expected feature compositions [required]" name="iexpectedfeatures" optional="False" type="data"/>
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77 <param format="qza,no_unzip.zip" label="--i-observed-features: ARTIFACT FeatureTable[RelativeFrequency] Observed feature compositions [required]" name="iobservedfeatures" optional="False" type="data"/>
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78 <param label="--p-depth: INTEGER Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 = root, 7 = species for the greengenes reference sequence database). [default: 7]" name="pdepth" optional="True" type="integer" value="7"/>
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79 <param label="--p-palette: " name="ppalette" 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="Set1">Set1</option>
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82 <option value="Set2">Set2</option>
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83 <option value="Set3">Set3</option>
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84 <option value="Pastel1">Pastel1</option>
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85 <option value="Pastel2">Pastel2</option>
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86 <option value="Paired">Paired</option>
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87 <option value="Accent">Accent</option>
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88 <option value="Dark2">Dark2</option>
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89 <option value="tab10">tab10</option>
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90 <option value="tab20">tab20</option>
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91 <option value="tab20b">tab20b</option>
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92 <option value="tab20c">tab20c</option>
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93 <option value="viridis">viridis</option>
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94 <option value="plasma">plasma</option>
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95 <option value="inferno">inferno</option>
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96 <option value="magma">magma</option>
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97 <option value="terrain">terrain</option>
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98 <option value="rainbow">rainbow</option>
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99 </param>
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100 <param label="--p-plot-tar: --p-no-plot-tar Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true positive features divided by the total number of observed features (TAR = true positives " name="pplottar" selected="False" type="boolean"/>
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101 <param label="--p-plot-tdr: --p-no-plot-tdr Plot taxon detection rate (TDR) on score plot. TDR is the number of true positive features divided by the total number of expected features (TDR = true positives " name="pplottdr" selected="False" type="boolean"/>
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102 <param label="--p-plot-r-value: --p-no-plot-r-value Plot expected vs. observed linear regression r value on score plot. [default: False]" name="pplotrvalue" selected="False" type="boolean"/>
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103 <param label="--p-no-plot-r-squared: Do not plot expected vs. observed linear regression r-squared value on score plot. [default: False]" name="pnoplotrsquared" selected="False" type="boolean"/>
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104 <param label="--p-plot-bray-curtis: --p-no-plot-bray-curtis Plot expected vs. observed Bray-Curtis dissimilarity scores on score plot. [default: False]" name="pplotbraycurtis" selected="False" type="boolean"/>
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105 <param label="--p-plot-jaccard: --p-no-plot-jaccard Plot expected vs. observed Jaccard distances scores on score plot. [default: False]" name="pplotjaccard" selected="False" type="boolean"/>
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106 <param label="--p-plot-observed-features: --p-no-plot-observed-features Plot observed features count on score plot. [default: False]" name="pplotobservedfeatures" selected="False" type="boolean"/>
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107 <param label="--p-no-plot-observed-features-ratio: Do not plot ratio of observed:expected features on score plot. [default: False]" name="pnoplotobservedfeaturesratio" selected="False" type="boolean"/>
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108 <param label="--m-metadata-column: COLUMN MetadataColumn[Categorical] Optional sample metadata that maps observed-features sample IDs to expected-features sample IDs. [optional]" name="mmetadatacolumn" optional="True" type="text"/>
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109
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110 <repeat name="input_files_mmetadatafile" optional="True" title="--m-metadata-file">
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111 <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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112 </repeat>
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113
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114 </inputs>
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115 <outputs>
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116 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
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117 </outputs>
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118 <help><![CDATA[
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119 Evaluate expected vs. observed taxonomic composition of samples
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120 ###############################################################
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121
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122 This visualizer compares the feature composition of pairs of observed and
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123 expected samples containing the same sample ID in two separate feature
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124 tables. Typically, feature composition will consist of taxonomy
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125 classifications or other semicolon-delimited feature annotations. Taxon
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126 accuracy rate, taxon detection rate, and linear regression scores between
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127 expected and observed observations are calculated at each semicolon-
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128 delimited rank, and plots of per-level accuracy and observation
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129 correlations are plotted. A histogram of distance between false positive
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130 observations and the nearest expected feature is also generated, where
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131 distance equals the number of rank differences between the observed feature
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132 and the nearest common lineage in the expected feature. This visualizer is
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133 most suitable for testing per-run data quality on sequencing runs that
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134 contain mock communities or other samples with known composition. Also
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135 suitable for sanity checks of bioinformatics pipeline performance.
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136
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137 Parameters
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138 ----------
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139 expected_features : FeatureTable[RelativeFrequency]
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140 Expected feature compositions
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141 observed_features : FeatureTable[RelativeFrequency]
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142 Observed feature compositions
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143 depth : Int, optional
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144 Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
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145 root, 7 = species for the greengenes reference sequence database).
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146 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
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147 Color palette to utilize for plotting.
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148 plot_tar : Bool, optional
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149 Plot taxon accuracy rate (TAR) on score plot. TAR is the number of true
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150 positive features divided by the total number of observed features (TAR
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151 = true positives / (true positives + false positives)).
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152 plot_tdr : Bool, optional
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153 Plot taxon detection rate (TDR) on score plot. TDR is the number of
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154 true positive features divided by the total number of expected features
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155 (TDR = true positives / (true positives + false negatives)).
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156 plot_r_value : Bool, optional
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157 Plot expected vs. observed linear regression r value on score plot.
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158 plot_r_squared : Bool, optional
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159 Plot expected vs. observed linear regression r-squared value on score
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160 plot.
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161 plot_bray_curtis : Bool, optional
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162 Plot expected vs. observed Bray-Curtis dissimilarity scores on score
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163 plot.
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164 plot_jaccard : Bool, optional
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165 Plot expected vs. observed Jaccard distances scores on score plot.
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166 plot_observed_features : Bool, optional
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167 Plot observed features count on score plot.
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168 plot_observed_features_ratio : Bool, optional
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169 Plot ratio of observed:expected features on score plot.
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170 metadata : MetadataColumn[Categorical], optional
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171 Optional sample metadata that maps observed_features sample IDs to
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172 expected_features sample IDs.
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173
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174 Returns
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175 -------
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176 visualization : Visualization
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177 ]]></help>
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178 <macros>
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179 <import>qiime_citation.xml</import>
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180 </macros>
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181 <expand macro="qiime_citation"/>
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182 </tool>
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