Mercurial > repos > q2d2 > qiime2__diversity_lib__beta_phylogenetic_meta_passthrough
changeset 3:c7ae6170043a draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
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--- a/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml Thu Jun 08 19:39:42 2023 +0000 +++ b/qiime2__diversity_lib__beta_phylogenetic_meta_passthrough.xml Thu Apr 25 21:01:55 2024 +0000 @@ -1,24 +1,24 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2023, QIIME 2 development team. +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: 2023.5.0) + q2galaxy (version: 2024.2.1) for: - qiime2 (version: 2023.5.1) + qiime2 (version: 2024.2.0) --> -<tool name="qiime2 diversity-lib beta-phylogenetic-meta-passthrough" id="qiime2__diversity_lib__beta_phylogenetic_meta_passthrough" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 diversity-lib beta-phylogenetic-meta-passthrough" id="qiime2__diversity_lib__beta_phylogenetic_meta_passthrough" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>Beta Phylogenetic Meta Passthrough</description> <requirements> - <container type="docker">quay.io/qiime2/core:2023.5</container> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> </requirements> <version_command>q2galaxy version diversity_lib</version_command> <command detect_errors="exit_code">q2galaxy run diversity_lib beta_phylogenetic_meta_passthrough '$inputs'</command> <configfiles> - <inputs name="inputs" data_style="paths"/> + <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="tables" type="data" format="qza" label="tables: List[FeatureTable[Frequency]]" help="[required] The feature tables containing the samples over which beta diversity should be computed." multiple="true"> @@ -40,18 +40,6 @@ <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> </param> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> - <conditional name="__q2galaxy__GUI__conditional__threads__"> - <param name="__q2galaxy__GUI__select__" type="select" label="threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."> - <option value="auto">auto (Str)</option> - <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option> - </param> - <when value="auto"> - <param name="threads" type="hidden" value="auto"/> - </when> - <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> - <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1] The number of CPU threads to use in performing this calculation. May not exceed the number of available physical cores. If threads = 'auto', one thread will be created for each identified CPU core on the host."/> - </when> - </conditional> <param name="variance_adjusted" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="variance_adjusted: Bool" help="[default: No] Perform variance adjustment based on Chang et al. BMC Bioinformatics 2011. Weights distances based on the proportion of the relative abundance represented between the samples at a given node under evaluation."/> <param name="alpha" type="float" min="0" max="1" optional="true" label="alpha: Float % Range(0, 1, inclusive_end=True)" help="[optional] This parameter is only used when the choice of metric is generalized_unifrac. The value of alpha controls importance of sample proportions. 1.0 is weighted normalized UniFrac. 0.0 is close to unweighted UniFrac, but only if the sample proportions are dichotomized."/> <param name="bypass_tips" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bypass_tips: Bool" help="[default: No] In a bifurcating tree, the tips make up about 50% of the nodes in a tree. By ignoring them, specificity can be traded for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs"/>