Mercurial > repos > q2d2 > qiime2__rescript__evaluate_classifications

annotate qiime2__rescript__evaluate_classifications.xml @ 2:0161f3d556a8 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:54:34 +0000
parents 73081ccaf0ff
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
1 <?xml version='1.0' encoding='utf-8'?>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
2 <!--
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
3 Copyright (c) 2024, QIIME 2 development team.
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
4
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
6 -->
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
7 <!--
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
8 This tool was automatically generated by:
2
0161f3d556a8 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
9 q2galaxy (version: 2024.10.0)
0
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
10 for:
2
0161f3d556a8 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
11 qiime2 (version: 2024.10.1)
0
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
12 -->
2
0161f3d556a8 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
13 <tool name="qiime2 rescript evaluate-classifications" id="qiime2__rescript__evaluate_classifications" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
0
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
14 <description>Interactively evaluate taxonomic classification accuracy.</description>
2
0161f3d556a8 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
15 <xrefs>
0161f3d556a8 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
16 <xref type="bio.tools">qiime2</xref>
0161f3d556a8 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
17 </xrefs>
0
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
18 <requirements>
2
0161f3d556a8 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 5f71b597c9495eae67a447744fded834f56ca1f7
q2d2
parents: 1
diff changeset
19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
0
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
20 </requirements>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
21 <version_command>q2galaxy version rescript</version_command>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
22 <command detect_errors="exit_code">q2galaxy run rescript evaluate_classifications '$inputs'</command>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
23 <configfiles>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
25 </configfiles>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
26 <inputs>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
27 <param name="expected_taxonomies" type="data" format="qza" label="expected_taxonomies: List[FeatureData[Taxonomy]]" help="[required] True taxonomic labels for one more more sets of features." multiple="true">
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
28 <options options_filter_attribute="metadata.semantic_type">
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
29 <filter type="add_value" value="FeatureData[Taxonomy]"/>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
30 </options>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
31 </param>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
32 <param name="observed_taxonomies" type="data" format="qza" label="observed_taxonomies: List[FeatureData[Taxonomy]]" help="[required] Predicted classifications of same sets of features, input in same order as expected_taxonomies." multiple="true">
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
33 <options options_filter_attribute="metadata.semantic_type">
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
34 <filter type="add_value" value="FeatureData[Taxonomy]"/>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
35 </options>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
36 </param>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
37 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
38 <repeat name="labels" help="[optional] List of labels to use for labeling evaluation results in the resulting visualization. Inputs are labeled with labels in the order that each is input. If there are fewer labels than inputs (or no labels), unnamed inputs are labeled numerically in sequential order. Extra labels are ignored." title="labels: List[Str]">
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
39 <param name="element" type="text" label="element: Str" help="[required]">
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
40 <sanitizer>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
41 <valid initial="string.printable"/>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
42 </sanitizer>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
43 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
44 </param>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
45 </repeat>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
46 </section>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
47 </inputs>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
48 <outputs>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
49 <data name="evaluation" format="qzv" label="${tool.name} on ${on_string}: evaluation.qzv" from_work_dir="evaluation.qzv"/>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
50 </outputs>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
51 <tests/>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
52 <help>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
53 QIIME 2: rescript evaluate-classifications
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
54 ==========================================
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
55 Interactively evaluate taxonomic classification accuracy.
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
56
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
57
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
58 Outputs:
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
59 --------
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
60 :evaluation.qzv: Visualization of classification accuracy results.
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
61
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
62 |
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
63
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
64 Description:
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
65 ------------
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
66 Evaluate taxonomic classification accuracy by comparing one or more sets of true taxonomic labels to the predicted taxonomies for the same set(s) of features. Output an interactive line plot of classification accuracy for each pair of expected/observed taxonomies. The x-axis in these plots represents the taxonomic levels present in the input taxonomies so are labeled numerically instead of by rank, but typically for 7-level taxonomies these will represent: 1 = domain/kingdom, 2 = phylum, 3 = class, 4 = order, 5 = family, 6 = genus, 7 = species.
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
67
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
68
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
69 |
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
70
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
71 </help>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
72 <citations>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
73 <citation type="doi">10.1186/s40168-018-0470-z</citation>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
74 <citation type="doi">10.1128/mSystems.00219-18</citation>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
75 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
76 <citation type="doi">10.1038/s41587-019-0209-9</citation>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
77 </citations>
9c36d1a88421 planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
q2d2
parents:
diff changeset
78 </tool>