Mercurial > repos > q2d2 > qiime2__phylogeny__raxml
diff qiime2__phylogeny__raxml.xml @ 0:5b4169c36760 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 20:15:31 +0000 |
| parents | |
| children | 1f553c9cc99e |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__phylogeny__raxml.xml Mon Aug 29 20:15:31 2022 +0000 @@ -0,0 +1,75 @@ +<?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 phylogeny raxml" id="qiime2__phylogeny__raxml" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Construct a phylogenetic tree with RAxML.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version phylogeny</version_command> + <command detect_errors="aggressive">q2galaxy run phylogeny raxml '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="alignment" type="data" format="qza" label="alignment: FeatureData[AlignedSequence]" help="[required] Aligned sequences to be used for phylogenetic reconstruction."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[AlignedSequence]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="seed" type="integer" optional="true" label="seed: Int" help="[optional] Random number seed for the parsimony starting tree. This allows you to reproduce tree results. If not supplied then one will be randomly chosen."/> + <param name="n_searches" type="integer" min="1" value="1" label="n_searches: Int % Range(1, None)" help="[default: 1] The number of independent maximum likelihood searches to perform. The single best scoring tree is returned."/> + <param name="n_threads" type="integer" min="1" value="1" label="n_threads: Int % Range(1, None)" help="[default: 1] The number of threads to use for multithreaded processing. Using more than one thread will enable the PTHREADS version of RAxML."/> + <param name="raxml_version" type="select" label="raxml_version: Str % Choices('Standard', 'SSE3', 'AVX2')" display="radio"> + <option value="Standard" selected="true">Standard</option> + <option value="SSE3">SSE3</option> + <option value="AVX2">AVX2</option> + </param> + <param name="substitution_model" type="select" label="substitution_model: Str % Choices('GTRGAMMA', 'GTRGAMMAI', 'GTRCAT', 'GTRCATI')" display="radio"> + <option value="GTRGAMMA" selected="true">GTRGAMMA</option> + <option value="GTRGAMMAI">GTRGAMMAI</option> + <option value="GTRCAT">GTRCAT</option> + <option value="GTRCATI">GTRCATI</option> + </param> + </section> + </inputs> + <outputs> + <data name="tree" format="qza" label="${tool.name} on ${on_string}: tree.qza" from_work_dir="tree.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: phylogeny raxml +======================== +Construct a phylogenetic tree with RAxML. + + +Outputs: +-------- +:tree.qza: The resulting phylogenetic tree. + +| + +Description: +------------ +Construct a phylogenetic tree with RAxML. See: https://sco.h-its.org/exelixis/web/software/raxml/ + + +| + +</help> + <citations> + <citation type="doi">10.1093/bioinformatics/btu033</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>