Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2-2020.8/qiime_quality-control_evaluate-taxonomy.xml @ 20:d93d8888f0b0 draft
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author | florianbegusch |
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date | Fri, 04 Sep 2020 12:44:24 +0000 |
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19:6c48f8d82424 | 20:d93d8888f0b0 |
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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> |