Mercurial > repos > q2d2 > qiime2__boots__alpha
changeset 0:dfb387d3bf55 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 17:07:32 +0000 |
| parents | |
| children | |
| files | qiime2__boots__alpha.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, 210 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__boots__alpha.xml Sat Nov 01 17:07:32 2025 +0000 @@ -0,0 +1,192 @@ +<?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 alpha" id="qiime2__boots__alpha" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause"> + <description>Perform resampled alpha diversity, returning average result vector.</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 alpha '$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="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="metric" type="select" label="metric: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'faith_pd', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'observed_features', 'osd', 'pielou_e', 'robbins', 'shannon', 'simpson', 'simpson_e', 'singles', 'strong')"> + <option value="__q2galaxy__::literal::None">Selection required</option> + <option value="ace">ace</option> + <option value="berger_parker_d">berger_parker_d</option> + <option value="brillouin_d">brillouin_d</option> + <option value="chao1">chao1</option> + <option value="chao1_ci">chao1_ci</option> + <option value="dominance">dominance</option> + <option value="doubles">doubles</option> + <option value="enspie">enspie</option> + <option value="esty_ci">esty_ci</option> + <option value="faith_pd">faith_pd</option> + <option value="fisher_alpha">fisher_alpha</option> + <option value="gini_index">gini_index</option> + <option value="goods_coverage">goods_coverage</option> + <option value="heip_e">heip_e</option> + <option value="kempton_taylor_q">kempton_taylor_q</option> + <option value="lladser_pe">lladser_pe</option> + <option value="margalef">margalef</option> + <option value="mcintosh_d">mcintosh_d</option> + <option value="mcintosh_e">mcintosh_e</option> + <option value="menhinick">menhinick</option> + <option value="michaelis_menten_fit">michaelis_menten_fit</option> + <option value="observed_features">observed_features</option> + <option value="osd">osd</option> + <option value="pielou_e">pielou_e</option> + <option value="robbins">robbins</option> + <option value="shannon">shannon</option> + <option value="simpson">simpson</option> + <option value="simpson_e">simpson_e</option> + <option value="singles">singles</option> + <option value="strong">strong</option> + <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> + </param> + <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="average_method" type="select" label="average_method: Str % Choices('mean', 'median')" display="radio"> + <option value="mean">mean</option> + <option value="median" selected="true">median</option> + </param> + </section> + </inputs> + <outputs> + <data name="average_alpha_diversity" format="qza" label="${tool.name} on ${on_string}: average_alpha_diversity.qza" from_work_dir="average_alpha_diversity.qza"/> + </outputs> + <tests> + <test> + <param name="table" value="alpha.test0.table.qza" ftype="qza"/> + <param name="sampling_depth" value="20"/> + <param name="metric" value="observed_features"/> + <param name="n" value="10"/> + <param name="replacement" value="__q2galaxy__::literal::True"/> + <param name="average_method" value="median"/> + <output name="average_alpha_diversity" ftype="qza"/> + </test> + <test> + <param name="table" value="alpha.test1.table.qza" ftype="qza"/> + <param name="sampling_depth" value="20"/> + <param name="metric" value="observed_features"/> + <param name="n" value="10"/> + <param name="replacement" value="__q2galaxy__::literal::False"/> + <param name="average_method" value="median"/> + <output name="average_alpha_diversity" ftype="qza"/> + </test> + </tests> + <help> +QIIME 2: boots alpha +==================== +Perform resampled alpha diversity, returning average result vector. + + +Outputs: +-------- +:average_alpha_diversity.qza: The average alpha diversity vector. + +| + +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 alpha diversity metric on each resulting `table`. The resulting artifacts are then averaged using the method specified by `average_method`, and the resulting average per-sample alpha diversities are returned. + +Examples: +--------- + +Bootstrapped observed features. +******************************* +Using the ``qiime2 boots alpha`` tool: + #. Set *"table"* to ``#: table.qza`` + #. Set *"sampling_depth"* to ``20`` + #. Set *"metric"* to ``observed_features`` + #. Set *"n"* to ``10`` + #. Set *"replacement"* to ``Yes`` + #. Expand the ``additional options`` section + + - Leave *"average_method"* as its default value of ``median`` + + #. 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 alpha [...] : average_alpha_diversity.qza`` + - ``observed-features-bootstrapped.qza`` + +Rarefaction-based observed features. +************************************ +Using the ``qiime2 boots alpha`` tool: + #. Set *"table"* to ``#: table.qza`` + #. Set *"sampling_depth"* to ``20`` + #. Set *"metric"* to ``observed_features`` + #. Set *"n"* to ``10`` + #. Set *"replacement"* to ``No`` + #. Expand the ``additional options`` section + + - Leave *"average_method"* as its default value of ``median`` + + #. 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 alpha [...] : average_alpha_diversity.qza`` + - ``observed-features-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 17:07:32 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 17:07:32 2025 +0000 @@ -0,0 +1,6 @@ +sample-id even-or-odd +#q2:types categorical +S1 odd +S2 even +S3 odd +S4 even