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comparison qiime2-2020.8/qiime_quality-control_evaluate-taxonomy.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_quality-control_evaluate-taxonomy" name="qiime quality-control evaluate-taxonomy"
3 version="2020.8">
4 <description>Evaluate expected vs. observed taxonomic assignments</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime quality-control evaluate-taxonomy
10
11 --i-expected-taxa=$iexpectedtaxa
12
13 --i-observed-taxa=$iobservedtaxa
14
15 #if $ifeaturetable:
16 --i-feature-table
17 #end if
18
19 --p-depth=$pdepth
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=$psampleid
35 #end if
36 --o-visualization=ovisualization
37
38 #if str($examples) != 'None':
39 --examples=$examples
40 #end if
41
42 ;
43 cp odatabase.qza $odatabase
44
45 ;
46 qiime tools export ovisualization.qzv --output-path out
47 && mkdir -p '$ovisualization.files_path'
48 && cp -r out/* '$ovisualization.files_path'
49 && mv '$ovisualization.files_path/index.html' '$ovisualization'
50
51 ;
52 qiime tools export ovisualization.qzv --output-path out
53 && mkdir -p '$ovisualization.files_path'
54 && cp -r out/* '$ovisualization.files_path'
55 && mv '$ovisualization.files_path/index.html' '$ovisualization'
56
57 ;
58 qiime tools export ovisualization.qzv --output-path out
59 && mkdir -p '$ovisualization.files_path'
60 && cp -r out/* '$ovisualization.files_path'
61 && mv '$ovisualization.files_path/index.html' '$ovisualization'
62
63 ]]></command>
64 <inputs>
65 <param format="qza,no_unzip.zip" label="--i-expected-taxa: ARTIFACT FeatureData[Taxonomy] Expected taxonomic assignments [required]" name="iexpectedtaxa" optional="False" type="data" />
66 <param format="qza,no_unzip.zip" label="--i-observed-taxa: ARTIFACT FeatureData[Taxonomy] Observed taxonomic assignments [required]" name="iobservedtaxa" optional="False" type="data" />
67 <param format="qza,no_unzip.zip" label="--i-feature-table: --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" selected="False" type="boolean" />
68 <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" type="text" />
69 <param label="--p-palette: " name="ppalette" optional="True" type="select">
70 <option selected="True" value="None">Selection is Optional</option>
71 <option value="Set1">Set1</option>
72 <option value="Set2">Set2</option>
73 <option value="Set3">Set3</option>
74 <option value="Pastel1">Pastel1</option>
75 <option value="Pastel2">Pastel2</option>
76 <option value="Paired">Paired</option>
77 <option value="Accent">Accent</option>
78 <option value="Dark2">Dark2</option>
79 <option value="tab10">tab10</option>
80 <option value="tab20">tab20</option>
81 <option value="tab20b">tab20b</option>
82 <option value="tab20c">tab20c</option>
83 <option value="viridis">viridis</option>
84 <option value="plasma">plasma</option>
85 <option value="inferno">inferno</option>
86 <option value="magma">magma</option>
87 <option value="terrain">terrain</option>
88 <option value="rainbow">rainbow</option>
89 </param>
90 <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: True]" name="pnorequireexpids" selected="False" type="boolean" />
91 <param label="--p-no-require-obs-ids: Do not require that all features found in expected taxa must be found in observed taxa or raise error. [default: True]" name="pnorequireobsids" selected="False" type="boolean" />
92 <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="False" type="text" />
93 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
94
95 </inputs>
96
97 <outputs>
98 <data format="html" label="${tool.name} on ${on_string}: visualization.html" name="ovisualization" />
99
100 </outputs>
101
102 <help><![CDATA[
103 Evaluate expected vs. observed taxonomic assignments
104 ###############################################################
105
106 This visualizer compares a pair of observed and expected taxonomic
107 assignments to calculate precision, recall, and F-measure at each taxonomic
108 level, up to maximum level specified by the depth parameter. These metrics
109 are calculated at each semicolon-delimited rank. This action is useful for
110 comparing the accuracy of taxonomic assignment, e.g., between different
111 taxonomy classifiers or other bioinformatics methods. Expected taxonomies
112 should be derived from simulated or mock community sequences that have
113 known taxonomic affiliations.
114
115 Parameters
116 ----------
117 expected_taxa : FeatureData[Taxonomy]
118 Expected taxonomic assignments
119 observed_taxa : FeatureData[Taxonomy]
120 Observed taxonomic assignments
121 depth : Int
122 Maximum depth of semicolon-delimited taxonomic ranks to test (e.g., 1 =
123 root, 7 = species for the greengenes reference sequence database).
124 palette : Str % Choices('Set1', 'Set2', 'Set3', 'Pastel1', 'Pastel2', 'Paired', 'Accent', 'Dark2', 'tab10', 'tab20', 'tab20b', 'tab20c', 'viridis', 'plasma', 'inferno', 'magma', 'terrain', 'rainbow'), optional
125 Color palette to utilize for plotting.
126 require_exp_ids : Bool, optional
127 Require that all features found in observed taxa must be found in
128 expected taxa or raise error.
129 require_obs_ids : Bool, optional
130 Require that all features found in expected taxa must be found in
131 observed taxa or raise error.
132 feature_table : FeatureTable[RelativeFrequency], optional
133 Optional feature table containing relative frequency of each feature,
134 used to weight accuracy scores by frequency. Must contain all features
135 found in expected and/or observed taxa. Features found in the table but
136 not the expected/observed taxa will be dropped prior to analysis.
137 sample_id : Str, optional
138 Optional sample ID to use for extracting frequency data from feature
139 table, and for labeling accuracy results. If no sample_id is provided,
140 feature frequencies are derived from the sum of all samples present in
141 the feature table.
142
143 Returns
144 -------
145 visualization : Visualization
146 ]]></help>
147 <macros>
148 <import>qiime_citation.xml</import>
149 </macros>
150 <expand macro="qiime_citation"/>
151 </tool>