| Previous changeset 2:26534bb91445 (2023-06-08) Next changeset 4:83d06804b15c (2024-06-03) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity commit 389df0134cd0763dcf02aac6e623fc15f8861c1e |
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modified:
qiime2__diversity__beta_phylogenetic.xml test-data/alpha_correlation.test0.alpha-div-faith-pd.qza test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza |
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| diff -r 26534bb91445 -r 0f15d1570213 qiime2__diversity__beta_phylogenetic.xml --- a/qiime2__diversity__beta_phylogenetic.xml Thu Jun 08 19:36:34 2023 +0000 +++ b/qiime2__diversity__beta_phylogenetic.xml Thu Apr 25 20:58:01 2024 +0000 |
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| @@ -1,31 +1,31 @@ <?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 beta-phylogenetic" id="qiime2__diversity__beta_phylogenetic" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 diversity beta-phylogenetic" id="qiime2__diversity__beta_phylogenetic" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>Beta diversity (phylogenetic)</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</version_command> <command detect_errors="exit_code">q2galaxy run diversity beta_phylogenetic '$inputs'</command> <configfiles> - <inputs name="inputs" data_style="paths"/> + <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency | PresenceAbsence]" help="[required] The feature table containing the samples over which beta diversity should be computed."> <options options_filter_attribute="metadata.semantic_type"> - <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> <filter type="add_value" value="FeatureTable[Frequency]"/> + <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> </param> @@ -44,18 +44,6 @@ <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"/> |
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| diff -r 26534bb91445 -r 0f15d1570213 test-data/alpha_group_significance.test0.alpha-div-faith-pd.qza |
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