# HG changeset patch
# User q2d2
# Date 1762016852 0
# Node ID dfb387d3bf55324e8fb28197dae0541557aace2f

planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__boots commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

diff -r 000000000000 -r dfb387d3bf55 qiime2__boots__alpha.xml
--- /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>
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diff -r 000000000000 -r dfb387d3bf55 test-data/beta_collection.test0.table.qza
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diff -r 000000000000 -r dfb387d3bf55 test-data/beta_collection.test1.table.qza
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diff -r 000000000000 -r dfb387d3bf55 test-data/core_metrics.test0.metadata.tsv
--- /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
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diff -r 000000000000 -r dfb387d3bf55 test-data/core_metrics.test1.metadata.tsv
--- /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
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diff -r 000000000000 -r dfb387d3bf55 test-data/kmer_diversity.test0.metadata.tsv
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kmer_diversity.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
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