Mercurial > repos > q2d2 > qiime2__fragment_insertion__classify_otus_experimental
comparison qiime2__fragment_insertion__classify_otus_experimental.xml @ 0:4139c3491d30 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 20:02:56 +0000 |
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children | 042aaca35af1 |
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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 fragment-insertion classify-otus-experimental" id="qiime2__fragment_insertion__classify_otus_experimental" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
14 <description>Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description> | |
15 <requirements> | |
16 <container type="docker">quay.io/qiime2/core:2022.8</container> | |
17 </requirements> | |
18 <version_command>q2galaxy version fragment_insertion</version_command> | |
19 <command detect_errors="aggressive">q2galaxy run fragment_insertion classify_otus_experimental '$inputs'</command> | |
20 <configfiles> | |
21 <inputs name="inputs" data_style="paths"/> | |
22 </configfiles> | |
23 <inputs> | |
24 <param name="representative_sequences" type="data" format="qza" label="representative_sequences: FeatureData[Sequence]" help="[required] The sequences used for a 'sepp' run to produce the 'tree'."> | |
25 <options options_filter_attribute="metadata.semantic_type"> | |
26 <filter type="add_value" value="FeatureData[Sequence]"/> | |
27 </options> | |
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> | |
29 </param> | |
30 <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted]" help="[required] The tree resulting from inserting fragments into a reference phylogeny, i.e. the output of function 'sepp'"> | |
31 <options options_filter_attribute="metadata.semantic_type"> | |
32 <filter type="add_value" value="Phylogeny[Rooted]"/> | |
33 </options> | |
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator> | |
35 </param> | |
36 <param name="reference_taxonomy" type="data" format="qza" label="reference_taxonomy: FeatureData[Taxonomy]" help="[required] Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string."> | |
37 <options options_filter_attribute="metadata.semantic_type"> | |
38 <filter type="add_value" value="FeatureData[Taxonomy]"/> | |
39 </options> | |
40 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> | |
41 </param> | |
42 </inputs> | |
43 <outputs> | |
44 <data name="classification" format="qza" label="${tool.name} on ${on_string}: classification.qza" from_work_dir="classification.qza"/> | |
45 </outputs> | |
46 <tests/> | |
47 <help> | |
48 QIIME 2: fragment-insertion classify-otus-experimental | |
49 ====================================================== | |
50 Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny. | |
51 | |
52 | |
53 Outputs: | |
54 -------- | |
55 :classification.qza: Taxonomic lineages for inserted fragments. | |
56 | |
57 | | |
58 | |
59 Description: | |
60 ------------ | |
61 Experimental: Use the resulting tree from 'sepp' and find closest OTU-ID for every inserted fragment. Then, look up the reference lineage string in the reference taxonomy. | |
62 | |
63 | |
64 | | |
65 | |
66 </help> | |
67 <citations> | |
68 <citation type="doi">10.1128/mSystems.00021-18</citation> | |
69 <citation type="doi">10.1371/journal.pone.0031009</citation> | |
70 <citation type="doi">10.1371/journal.pcbi.1002195</citation> | |
71 <citation type="bibtex">@article{cite4, | |
72 author = {Matsen, Frederick A and Kodner, Robin B and Armbrust, E Virginia}, | |
73 journal = {BMC bioinformatics}, | |
74 number = {1}, | |
75 pages = {538}, | |
76 publisher = {BioMed Central}, | |
77 title = {pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree}, | |
78 volume = {11}, | |
79 year = {2010} | |
80 } | |
81 </citation> | |
82 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
83 </citations> | |
84 </tool> |