2
+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_quality-control_evaluate-taxonomy" name="qiime quality-control evaluate-taxonomy" version="2019.4">
+ − 3 <description> - Evaluate expected vs. observed taxonomic assignments</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2019.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command><![CDATA[
+ − 8 qiime quality-control evaluate-taxonomy
+ − 9
+ − 10 --i-expected-taxa=$iexpectedtaxa
+ − 11 --i-observed-taxa=$iobservedtaxa
4
+ − 12
+ − 13 #if str($pdepth):
+ − 14 --p-depth="$pdepth"
+ − 15 #end if
2
+ − 16
+ − 17 #if str($ifeaturetable) != 'None':
+ − 18 --i-feature-table=$ifeaturetable
+ − 19 #end if
+ − 20
+ − 21 #if str($ppalette) != 'None':
+ − 22 --p-palette=$ppalette
+ − 23 #end if
+ − 24
+ − 25 #if $pnorequireexpids:
+ − 26 --p-no-require-exp-ids
+ − 27 #end if
+ − 28
+ − 29 #if $pnorequireobsids:
+ − 30 --p-no-require-obs-ids
+ − 31 #end if
+ − 32
+ − 33 #if str($psampleid):
+ − 34 --p-sample-id="$psampleid"
+ − 35 #end if
+ − 36
+ − 37 --o-visualization=ovisualization
+ − 38 ;
+ − 39 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
+ − 40 && cp -r out/* '$ovisualization.files_path'
+ − 41 && mv '$ovisualization.files_path/index.html' '$ovisualization'
+ − 42 ]]></command>
+ − 43 <inputs>
+ − 44 <param format="qza,no_unzip.zip" label="--i-expected-taxa: ARTIFACT FeatureData[Taxonomy] Expected taxonomic assignments [required]" name="iexpectedtaxa" optional="False" type="data"/>
+ − 45 <param format="qza,no_unzip.zip" label="--i-observed-taxa: ARTIFACT FeatureData[Taxonomy] Observed taxonomic assignments [required]" name="iobservedtaxa" optional="False" type="data"/>
+ − 46 <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). [required]" name="pdepth" optional="False" value="" type="integer"/>
+ − 47 <param format="qza,no_unzip.zip" label="--i-feature-table: ARTIFACT FeatureTable[RelativeFrequency] Optional feature table containing relative frequency of each feature, used to weight accuracy scores by frequency. Must contain all features found in expected and/or observed taxa. Features found in the table but not the expected/observed taxa will be dropped prior to analysis. [optional]" name="ifeaturetable" optional="True" type="data"/>
+ − 48 <param label="--p-palette: " name="ppalette" optional="True" type="select">
+ − 49 <option selected="True" value="None">Selection is Optional</option>
+ − 50 <option value="Set1">Set1</option>
+ − 51 <option value="Set2">Set2</option>
+ − 52 <option value="Set3">Set3</option>
+ − 53 <option value="Pastel1">Pastel1</option>
+ − 54 <option value="Pastel2">Pastel2</option>
+ − 55 <option value="Paired">Paired</option>
+ − 56 <option value="Accent">Accent</option>
+ − 57 <option value="Dark2">Dark2</option>
+ − 58 <option value="tab10">tab10</option>
+ − 59 <option value="tab20">tab20</option>
+ − 60 <option value="tab20b">tab20b</option>
+ − 61 <option value="tab20c">tab20c</option>
+ − 62 <option value="viridis">viridis</option>
+ − 63 <option value="plasma">plasma</option>
+ − 64 <option value="inferno">inferno</option>
+ − 65 <option value="magma">magma</option>
+ − 66 <option value="terrain">terrain</option>
+ − 67 <option value="rainbow">rainbow</option>
+ − 68 </param>
+ − 69 <param label="--p-no-require-exp-ids: Do not require that all features found in observed taxa must be found in expected taxa or raise error. [default: False]" name="pnorequireexpids" selected="False" type="boolean"/>
+ − 70 <param label="--p-no-require-obs-ids: Require that all features found in expected taxa must be found in observed taxa or raise error. [default: False]" name="pnorequireobsids" selected="False" type="boolean"/>
+ − 71 <param label="--p-sample-id: TEXT Optional sample ID to use for extracting frequency data from feature table, and for labeling accuracy results. If no sample-id is provided, feature frequencies are derived from the sum of all samples present in the feature table. [optional]" name="psampleid" optional="True" type="text"/>
+ − 72 </inputs>
+ − 73 <outputs>
+ − 74 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
+ − 75 </outputs>
+ − 76 <help><![CDATA[
+ − 77 Evaluate expected vs. observed taxonomic assignments
+ − 78 ####################################################
+ − 79
+ − 80 This visualizer compares a pair of observed and expected taxonomic
+ − 81 assignments to calculate precision, recall, and F-measure at each taxonomic
+ − 82 level, up to maximum level specified by the depth parameter. These metrics
+ − 83 are calculated at each semicolon-delimited rank. This action is useful for
+ − 84 comparing the accuracy of taxonomic assignment, e.g., between different
+ − 85 taxonomy classifiers or other bioinformatics methods. Expected taxonomies
+ − 86 should be derived from simulated or mock community sequences that have
+ − 87 known taxonomic affiliations.
+ − 88
+ − 89 Parameters
+ − 90 ----------
+ − 91 expected_taxa : FeatureData[Taxonomy]
+ − 92 Expected taxonomic assignments
+ − 93 observed_taxa : FeatureData[Taxonomy]
+ − 94 Observed taxonomic assignments
+ − 95 depth : Int
+ − 96 Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
+ − 97 root, 7 = species for the greengenes reference sequence database).
+ − 98 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
+ − 99 Color palette to utilize for plotting.
+ − 100 require_exp_ids : Bool, optional
+ − 101 Require that all features found in observed taxa must be found in
+ − 102 expected taxa or raise error.
+ − 103 require_obs_ids : Bool, optional
+ − 104 Require that all features found in expected taxa must be found in
+ − 105 observed taxa or raise error.
+ − 106 feature_table : FeatureTable[RelativeFrequency], optional
+ − 107 Optional feature table containing relative frequency of each feature,
+ − 108 used to weight accuracy scores by frequency. Must contain all features
+ − 109 found in expected and/or observed taxa. Features found in the table but
+ − 110 not the expected/observed taxa will be dropped prior to analysis.
+ − 111 sample_id : Str, optional
+ − 112 Optional sample ID to use for extracting frequency data from feature
+ − 113 table, and for labeling accuracy results. If no sample_id is provided,
+ − 114 feature frequencies are derived from the sum of all samples present in
+ − 115 the feature table.
+ − 116
+ − 117 Returns
+ − 118 -------
+ − 119 visualization : Visualization
+ − 120 ]]></help>
+ − 121 <macros>
+ − 122 <import>qiime_citation.xml</import>
+ − 123 </macros>
+ − 124 <expand macro="qiime_citation"/>
+ − 125 </tool>
