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comparison qiime2/qiime_quality-control_evaluate-taxonomy.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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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
12 --p-depth="$pdepth"
13
14 #if str($ifeaturetable) != 'None':
15 --i-feature-table=$ifeaturetable
16 #end if
17
18 #if str($ppalette) != 'None':
19 --p-palette=$ppalette
20 #end if
21
22 #if $pnorequireexpids:
23 --p-no-require-exp-ids
24 #end if
25
26 #if $pnorequireobsids:
27 --p-no-require-obs-ids
28 #end if
29
30 #if str($psampleid):
31 --p-sample-id="$psampleid"
32 #end if
33
34 --o-visualization=ovisualization
35 ;
36 qiime tools export --input-path ovisualization.qzv --output-path out && mkdir -p '$ovisualization.files_path'
37 && cp -r out/* '$ovisualization.files_path'
38 && mv '$ovisualization.files_path/index.html' '$ovisualization'
39 ]]></command>
40 <inputs>
41 <param format="qza,no_unzip.zip" label="--i-expected-taxa: ARTIFACT FeatureData[Taxonomy] Expected taxonomic assignments [required]" name="iexpectedtaxa" optional="False" type="data"/>
42 <param format="qza,no_unzip.zip" label="--i-observed-taxa: ARTIFACT FeatureData[Taxonomy] Observed taxonomic assignments [required]" name="iobservedtaxa" optional="False" type="data"/>
43 <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"/>
44 <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"/>
45 <param label="--p-palette: " name="ppalette" optional="True" type="select">
46 <option selected="True" value="None">Selection is Optional</option>
47 <option value="Set1">Set1</option>
48 <option value="Set2">Set2</option>
49 <option value="Set3">Set3</option>
50 <option value="Pastel1">Pastel1</option>
51 <option value="Pastel2">Pastel2</option>
52 <option value="Paired">Paired</option>
53 <option value="Accent">Accent</option>
54 <option value="Dark2">Dark2</option>
55 <option value="tab10">tab10</option>
56 <option value="tab20">tab20</option>
57 <option value="tab20b">tab20b</option>
58 <option value="tab20c">tab20c</option>
59 <option value="viridis">viridis</option>
60 <option value="plasma">plasma</option>
61 <option value="inferno">inferno</option>
62 <option value="magma">magma</option>
63 <option value="terrain">terrain</option>
64 <option value="rainbow">rainbow</option>
65 </param>
66 <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"/>
67 <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"/>
68 <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"/>
69 </inputs>
70 <outputs>
71 <data format="html" label="${tool.name} on ${on_string}: visualization.qzv" name="ovisualization"/>
72 </outputs>
73 <help><![CDATA[
74 Evaluate expected vs. observed taxonomic assignments
75 ####################################################
76
77 This visualizer compares a pair of observed and expected taxonomic
78 assignments to calculate precision, recall, and F-measure at each taxonomic
79 level, up to maximum level specified by the depth parameter. These metrics
80 are calculated at each semicolon-delimited rank. This action is useful for
81 comparing the accuracy of taxonomic assignment, e.g., between different
82 taxonomy classifiers or other bioinformatics methods. Expected taxonomies
83 should be derived from simulated or mock community sequences that have
84 known taxonomic affiliations.
85
86 Parameters
87 ----------
88 expected_taxa : FeatureData[Taxonomy]
89 Expected taxonomic assignments
90 observed_taxa : FeatureData[Taxonomy]
91 Observed taxonomic assignments
92 depth : Int
93 Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
94 root, 7 = species for the greengenes reference sequence database).
95 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
96 Color palette to utilize for plotting.
97 require_exp_ids : Bool, optional
98 Require that all features found in observed taxa must be found in
99 expected taxa or raise error.
100 require_obs_ids : Bool, optional
101 Require that all features found in expected taxa must be found in
102 observed taxa or raise error.
103 feature_table : FeatureTable[RelativeFrequency], optional
104 Optional feature table containing relative frequency of each feature,
105 used to weight accuracy scores by frequency. Must contain all features
106 found in expected and/or observed taxa. Features found in the table but
107 not the expected/observed taxa will be dropped prior to analysis.
108 sample_id : Str, optional
109 Optional sample ID to use for extracting frequency data from feature
110 table, and for labeling accuracy results. If no sample_id is provided,
111 feature frequencies are derived from the sum of all samples present in
112 the feature table.
113
114 Returns
115 -------
116 visualization : Visualization
117 ]]></help>
118 <macros>
119 <import>qiime_citation.xml</import>
120 </macros>
121 <expand macro="qiime_citation"/>
122 </tool>