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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author | q2d2 |
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date | Thu, 25 Apr 2024 21:15:00 +0000 |
parents | 52cffcc84c14 |
children | 2821f5e19fe7 |
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<?xml version='1.0' encoding='utf-8'?> <!-- Copyright (c) 2024, QIIME 2 development team. Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) --> <!-- This tool was automatically generated by: q2galaxy (version: 2024.2.1) for: qiime2 (version: 2024.2.0) --> <tool name="qiime2 fragment-insertion classify-otus-experimental" id="qiime2__fragment_insertion__classify_otus_experimental" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description> <requirements> <container type="docker">quay.io/qiime2/amplicon:2024.2</container> </requirements> <version_command>q2galaxy version fragment_insertion</version_command> <command detect_errors="exit_code">q2galaxy run fragment_insertion classify_otus_experimental '$inputs'</command> <configfiles> <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="representative_sequences" type="data" format="qza" label="representative_sequences: FeatureData[Sequence]" help="[required] The sequences used for a 'sepp' run to produce the 'tree'."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureData[Sequence]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> </param> <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted]" help="[required] The tree resulting from inserting fragments into a reference phylogeny, i.e. the output of function 'sepp'"> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="Phylogeny[Rooted]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator> </param> <param name="reference_taxonomy" type="data" format="qza" label="reference_taxonomy: FeatureData[Taxonomy]" help="[required] Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureData[Taxonomy]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> </param> </inputs> <outputs> <data name="classification" format="qza" label="${tool.name} on ${on_string}: classification.qza" from_work_dir="classification.qza"/> </outputs> <tests/> <help> QIIME 2: fragment-insertion classify-otus-experimental ====================================================== Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny. Outputs: -------- :classification.qza: Taxonomic lineages for inserted fragments. | Description: ------------ 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. | </help> <citations> <citation type="doi">10.1128/mSystems.00021-18</citation> <citation type="doi">10.1371/journal.pone.0031009</citation> <citation type="doi">10.1371/journal.pcbi.1002195</citation> <citation type="bibtex">@article{cite4, author = {Matsen, Frederick A and Kodner, Robin B and Armbrust, E Virginia}, journal = {BMC bioinformatics}, number = {1}, pages = {538}, publisher = {BioMed Central}, title = {pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree}, volume = {11}, year = {2010} } </citation> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>