Mercurial > repos > q2d2 > qiime2__taxa__collapse
comparison qiime2__taxa__collapse.xml @ 0:3e34b8065c52 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__taxa commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 20:29:53 +0000 |
| parents | |
| children | 96d3a6a511bc |
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| -1:000000000000 | 0:3e34b8065c52 |
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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 taxa collapse" id="qiime2__taxa__collapse" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
| 14 <description>Collapse features by their taxonomy at the specified level</description> | |
| 15 <requirements> | |
| 16 <container type="docker">quay.io/qiime2/core:2022.8</container> | |
| 17 </requirements> | |
| 18 <version_command>q2galaxy version taxa</version_command> | |
| 19 <command detect_errors="aggressive">q2galaxy run taxa collapse '$inputs'</command> | |
| 20 <configfiles> | |
| 21 <inputs name="inputs" data_style="paths"/> | |
| 22 </configfiles> | |
| 23 <inputs> | |
| 24 <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table to be collapsed."> | |
| 25 <options options_filter_attribute="metadata.semantic_type"> | |
| 26 <filter type="add_value" value="FeatureTable[Frequency]"/> | |
| 27 </options> | |
| 28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> | |
| 29 </param> | |
| 30 <param name="taxonomy" type="data" format="qza" label="taxonomy: FeatureData[Taxonomy]" help="[required] Taxonomic annotations for features in the provided feature table. All features in the feature table must have a corresponding taxonomic annotation. Taxonomic annotations that are not present in the feature table will be ignored."> | |
| 31 <options options_filter_attribute="metadata.semantic_type"> | |
| 32 <filter type="add_value" value="FeatureData[Taxonomy]"/> | |
| 33 </options> | |
| 34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> | |
| 35 </param> | |
| 36 <param name="level" type="integer" value="" label="level: Int" help="[required] The taxonomic level at which the features should be collapsed. All ouput features will have exactly this many levels of taxonomic annotation."/> | |
| 37 </inputs> | |
| 38 <outputs> | |
| 39 <data name="collapsed_table" format="qza" label="${tool.name} on ${on_string}: collapsed_table.qza" from_work_dir="collapsed_table.qza"/> | |
| 40 </outputs> | |
| 41 <tests/> | |
| 42 <help> | |
| 43 QIIME 2: taxa collapse | |
| 44 ====================== | |
| 45 Collapse features by their taxonomy at the specified level | |
| 46 | |
| 47 | |
| 48 Outputs: | |
| 49 -------- | |
| 50 :collapsed_table.qza: The resulting feature table, where all features are now taxonomic annotations with the user-specified number of levels. | |
| 51 | |
| 52 | | |
| 53 | |
| 54 Description: | |
| 55 ------------ | |
| 56 Collapse groups of features that have the same taxonomic assignment through the specified level. The frequencies of all features will be summed when they are collapsed. | |
| 57 | |
| 58 | |
| 59 | | |
| 60 | |
| 61 </help> | |
| 62 <citations> | |
| 63 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
| 64 </citations> | |
| 65 </tool> |