Mercurial > repos > q2d2 > qiime2__emperor__procrustes_plot
comparison qiime2__emperor__procrustes_plot.xml @ 0:7c4129b3c5ea draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
---|---|
date | Mon, 29 Aug 2022 19:48:36 +0000 |
parents | |
children | bd0dbc487394 |
comparison
equal
deleted
inserted
replaced
-1:000000000000 | 0:7c4129b3c5ea |
---|---|
1 <?xml version='1.0' encoding='utf-8'?> | |
2 <!-- | |
3 Copyright (c) 2022, QIIME 2 development team. | |
4 | |
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) | |
6 --> | |
7 <!-- | |
8 This tool was automatically generated by: | |
9 q2galaxy (version: 2022.8.1) | |
10 for: | |
11 qiime2 (version: 2022.8.1) | |
12 --> | |
13 <tool name="qiime2 emperor procrustes-plot" id="qiime2__emperor__procrustes_plot" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
14 <description>Visualize and Interact with a procrustes plot</description> | |
15 <requirements> | |
16 <container type="docker">quay.io/qiime2/core:2022.8</container> | |
17 </requirements> | |
18 <version_command>q2galaxy version emperor</version_command> | |
19 <command detect_errors="aggressive">q2galaxy run emperor procrustes_plot '$inputs'</command> | |
20 <configfiles> | |
21 <inputs name="inputs" data_style="paths"/> | |
22 </configfiles> | |
23 <inputs> | |
24 <param name="reference_pcoa" type="data" format="qza" label="reference_pcoa: PCoAResults" help="[required] The reference ordination matrix to be plotted."> | |
25 <options options_filter_attribute="metadata.semantic_type"> | |
26 <filter type="add_value" value="PCoAResults"/> | |
27 </options> | |
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</validator> | |
29 </param> | |
30 <param name="other_pcoa" type="data" format="qza" label="other_pcoa: PCoAResults" help="[required] The "other" ordination matrix to be plotted (the one that was fitted to the reference)."> | |
31 <options options_filter_attribute="metadata.semantic_type"> | |
32 <filter type="add_value" value="PCoAResults"/> | |
33 </options> | |
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</validator> | |
35 </param> | |
36 <repeat name="metadata" min="1" help="[required] The sample metadata." title="metadata: Metadata"> | |
37 <conditional name="__q2galaxy__GUI__conditional__metadata__"> | |
38 <param name="type" type="select" label="metadata: Metadata"> | |
39 <option value="tsv" selected="true">Metadata from TSV</option> | |
40 <option value="qza">Metadata from Artifact</option> | |
41 </param> | |
42 <when value="tsv"> | |
43 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> | |
44 </when> | |
45 <when value="qza"> | |
46 <param name="source" type="data" format="qza" label="Metadata Source"/> | |
47 </when> | |
48 </conditional> | |
49 </repeat> | |
50 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
51 <param name="m2_stats" type="data" format="qza" optional="true" label="m2_stats: ProcrustesStatistics" help="[optional] The M^2 value of the procrustes analysis & its associated p value."> | |
52 <options options_filter_attribute="metadata.semantic_type"> | |
53 <filter type="add_value" value="ProcrustesStatistics"/> | |
54 </options> | |
55 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['ProcrustesStatistics']</validator> | |
56 </param> | |
57 <repeat name="custom_axes" help="[optional] Numeric sample metadata columns that should be included as axes in the Emperor plot." title="custom_axes: List[Str]"> | |
58 <param name="element" type="text" label="element: Str" help="[required]"> | |
59 <sanitizer> | |
60 <valid initial="string.printable"/> | |
61 </sanitizer> | |
62 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> | |
63 </param> | |
64 </repeat> | |
65 <param name="ignore_missing_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_missing_samples: Bool" help="[default: No] This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata."/> | |
66 </section> | |
67 </inputs> | |
68 <outputs> | |
69 <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> | |
70 </outputs> | |
71 <tests/> | |
72 <help> | |
73 QIIME 2: emperor procrustes-plot | |
74 ================================ | |
75 Visualize and Interact with a procrustes plot | |
76 | |
77 | |
78 Outputs: | |
79 -------- | |
80 :visualization.qzv: <no description> | |
81 | |
82 | | |
83 | |
84 Description: | |
85 ------------ | |
86 Plot two procrustes-fitted matrices | |
87 | |
88 | |
89 | | |
90 | |
91 </help> | |
92 <citations> | |
93 <citation type="doi">10.1186/2047-217X-2-16</citation> | |
94 <citation type="doi">10.1016/j.chom.2016.12.009</citation> | |
95 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
96 </citations> | |
97 </tool> |