Mercurial > repos > q2d2 > qiime2__boots__beta_collection
changeset 0:cb82cee9add2 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__boots commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b
| author | q2d2 |
|---|---|
| date | Sat, 01 Nov 2025 17:08:24 +0000 |
| parents | |
| children | |
| files | qiime2__boots__beta_collection.xml test-data/alpha.test0.table.qza test-data/alpha.test1.table.qza test-data/beta_collection.test0.table.qza test-data/beta_collection.test1.table.qza test-data/core_metrics.test0.metadata.tsv test-data/core_metrics.test0.table.qza test-data/core_metrics.test1.metadata.tsv test-data/core_metrics.test1.table.qza test-data/kmer_diversity.test0.metadata.tsv test-data/kmer_diversity.test0.sequences.qza test-data/kmer_diversity.test0.table.qza test-data/resample.test0.table.qza test-data/resample.test1.table.qza |
| diffstat | 14 files changed, 208 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__boots__beta_collection.xml Sat Nov 01 17:08:24 2025 +0000 @@ -0,0 +1,190 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2025, 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: 2025.10.0) +for: + qiime2 (version: 2025.10.0) +--> +<tool name="qiime2 boots beta-collection" id="qiime2__boots__beta_collection" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause"> + <description>Perform resampled beta diversity, returning `n` distance matrices.</description> + <xrefs> + <xref type="bio.tools">qiime2</xref> + </xrefs> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2025.10</container> + </requirements> + <version_command>q2galaxy version boots</version_command> + <command detect_errors="exit_code">q2galaxy run boots beta_collection '$inputs'</command> + <configfiles> + <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 input feature table."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> + <filter type="add_value" value="FeatureTable[Frequency]"/> + <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> + </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> + <param name="metric" type="select" label="metric: Str % Choices('aitchison', 'braycurtis', 'canberra', 'canberra_adkins', 'chebyshev', 'cityblock', 'correlation', 'cosine', 'dice', 'euclidean', 'generalized_unifrac', 'hamming', 'jaccard', 'jensenshannon', 'matching', 'minkowski', 'rogerstanimoto', 'russellrao', 'seuclidean', 'sokalmichener', 'sokalsneath', 'sqeuclidean', 'unweighted_unifrac', 'weighted_normalized_unifrac', 'weighted_unifrac', 'yule')"> + <option value="__q2galaxy__::literal::None">Selection required</option> + <option value="aitchison">aitchison</option> + <option value="braycurtis">braycurtis</option> + <option value="canberra">canberra</option> + <option value="canberra_adkins">canberra_adkins</option> + <option value="chebyshev">chebyshev</option> + <option value="cityblock">cityblock</option> + <option value="correlation">correlation</option> + <option value="cosine">cosine</option> + <option value="dice">dice</option> + <option value="euclidean">euclidean</option> + <option value="generalized_unifrac">generalized_unifrac</option> + <option value="hamming">hamming</option> + <option value="jaccard">jaccard</option> + <option value="jensenshannon">jensenshannon</option> + <option value="matching">matching</option> + <option value="minkowski">minkowski</option> + <option value="rogerstanimoto">rogerstanimoto</option> + <option value="russellrao">russellrao</option> + <option value="seuclidean">seuclidean</option> + <option value="sokalmichener">sokalmichener</option> + <option value="sokalsneath">sokalsneath</option> + <option value="sqeuclidean">sqeuclidean</option> + <option value="unweighted_unifrac">unweighted_unifrac</option> + <option value="weighted_normalized_unifrac">weighted_normalized_unifrac</option> + <option value="weighted_unifrac">weighted_unifrac</option> + <option value="yule">yule</option> + <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> + </param> + <param name="sampling_depth" type="integer" min="1" value="" label="sampling_depth: Int % Range(1, None)" help="[required] The total number of observations that each sample in `table` should be resampled to. Samples where the total number of observations in `table` is less than `sampling_depth` will be not be included in the output tables."/> + <param name="n" type="integer" min="1" value="" label="n: Int % Range(1, None)" help="[required] The number of resampled tables that should be generated."/> + <param name="replacement" type="select" label="replacement: Bool" help="[required] Resample `table` with replacement (i.e., bootstrap) or without replacement (i.e., rarefaction)." display="radio"> + <option value="__q2galaxy__::literal::None">Selection required</option> + <option value="__q2galaxy__::literal::True">Yes</option> + <option value="__q2galaxy__::literal::False">No</option> + <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"> + <param name="phylogeny" type="data" format="qza" optional="true" label="phylogeny: Phylogeny[Rooted]" help="[optional] The phylogenetic tree to use in phylogenetic diversity calculations. All feature ids in `table` must be present in this tree, but this tree can contain feature ids that are not present in `table`."> + <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="bypass_tips" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="bypass_tips: Bool" help="[default: No] Ignore tips of tree in phylogenetic diversity calculations, trading specificity for reduced compute time. This has the effect of collapsing the phylogeny, and is analogous (in concept) to moving from 99% to 97% OTUs."/> + <param name="pseudocount" type="integer" min="1" value="1" label="pseudocount: Int % Range(1, None)" help="[default: 1] A pseudocount to handle zeros for compositional metrics. This is ignored for other metrics."/> + <param name="alpha" type="float" min="0" max="1" optional="true" label="alpha: Float % Range(0, 1, inclusive_end=True)" help="[optional] The alpha value used with the generalized UniFrac metric."/> + <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) for phylogenetic diversity metrics."/> + </section> + </inputs> + <outputs> + <collection name="distance_matrices" type="list"> + <discover_datasets directory="distance_matrices" pattern="__name_and_ext__"/> + </collection> + </outputs> + <tests> + <test> + <param name="table" value="beta_collection.test0.table.qza" ftype="qza"/> + <param name="metric" value="braycurtis"/> + <param name="sampling_depth" value="20"/> + <param name="n" value="10"/> + <param name="replacement" value="__q2galaxy__::literal::True"/> + <param name="average_method" value="medoid"/> + <output name="average_distance_matrix" ftype="qza"/> + </test> + <test> + <param name="table" value="beta_collection.test1.table.qza" ftype="qza"/> + <param name="metric" value="braycurtis"/> + <param name="sampling_depth" value="20"/> + <param name="n" value="10"/> + <param name="replacement" value="__q2galaxy__::literal::False"/> + <param name="average_method" value="medoid"/> + <output name="average_distance_matrix" ftype="qza"/> + </test> + </tests> + <help> +QIIME 2: boots beta-collection +============================== +Perform resampled beta diversity, returning `n` distance matrices. + + +Outputs: +-------- +:distance_matrices.qza: `n` beta diversity distance matrices, each containing distances between all pairs of samples and computed from resampled feature tables. + +| + +Description: +------------ +Given a single feature table as input, this action resamples the feature table `n` times to a total frequency of `sampling depth` per sample, and then computes the specified beta diversity metric on each resulting `table`. The resulting artifacts can be used, for example, to explore the variance across `n` iterations of resampling. + +Examples: +--------- + +Bootstrapped Bray-Curtis. +************************* +Using the ``qiime2 boots beta`` tool: + #. Set *"table"* to ``#: table.qza`` + #. Set *"metric"* to ``braycurtis`` + #. Set *"sampling_depth"* to ``20`` + #. Set *"n"* to ``10`` + #. Set *"replacement"* to ``Yes`` + #. Expand the ``additional options`` section + + - Set *"average_method"* to ``medoid`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 boots beta [...] : average_distance_matrix.qza`` + - ``braycurtis-bootstrapped.qza`` + +Rarefaction-based Bray-Curtis. +****************************** +Using the ``qiime2 boots beta`` tool: + #. Set *"table"* to ``#: table.qza`` + #. Set *"metric"* to ``braycurtis`` + #. Set *"sampling_depth"* to ``20`` + #. Set *"n"* to ``10`` + #. Set *"replacement"* to ``No`` + #. Expand the ``additional options`` section + + - Set *"average_method"* to ``medoid`` + + #. Press the ``Execute`` button. + +Once completed, for the new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 boots beta [...] : average_distance_matrix.qza`` + - ``braycurtis-rarefaction.qza`` + + +| + +</help> + <citations> + <citation type="doi">https://doi.org/10.12688/f1000research.156295.1</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/core_metrics.test0.metadata.tsv Sat Nov 01 17:08:24 2025 +0000 @@ -0,0 +1,6 @@ +sample-id even-or-odd +#q2:types categorical +S1 odd +S2 even +S3 odd +S4 even
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/core_metrics.test1.metadata.tsv Sat Nov 01 17:08:24 2025 +0000 @@ -0,0 +1,6 @@ +sample-id even-or-odd +#q2:types categorical +S1 odd +S2 even +S3 odd +S4 even