| Next changeset 1:042aaca35af1 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__fragment_insertion commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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qiime2__fragment_insertion__classify_otus_experimental.xml test-data/.gitkeep |
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| diff -r 000000000000 -r 4139c3491d30 qiime2__fragment_insertion__classify_otus_experimental.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__fragment_insertion__classify_otus_experimental.xml Mon Aug 29 20:02:56 2022 +0000 |
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| @@ -0,0 +1,84 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2022, 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: 2022.8.1) +for: + qiime2 (version: 2022.8.1) +--> +<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"> + <description>Experimental: Obtain taxonomic lineages, by finding closest OTU in reference phylogeny.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version fragment_insertion</version_command> + <command detect_errors="aggressive">q2galaxy run fragment_insertion classify_otus_experimental '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="representative_sequences" type="data" format="qza" label="representative_sequences: FeatureData[Sequence]" help="[required] The sequences used for a 'sepp' run to produce the 'tree'."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[Sequence]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> + </param> + <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted]" help="[required] The tree resulting from inserting fragments into a reference phylogeny, i.e. the output of function 'sepp'"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="Phylogeny[Rooted]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]']</validator> + </param> + <param name="reference_taxonomy" type="data" format="qza" label="reference_taxonomy: FeatureData[Taxonomy]" help="[required] Reference taxonomic table that maps every OTU-ID into a taxonomic lineage string."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[Taxonomy]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Taxonomy]']</validator> + </param> + </inputs> + <outputs> + <data name="classification" format="qza" label="${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> |