# HG changeset patch
# User q2d2
# Date 1762016838 0
# Node ID 75593c55ca60eab5536bfc244549e3fa1835b009

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

diff -r 000000000000 -r 75593c55ca60 qiime2__boots__core_metrics.xml
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__boots__core_metrics.xml	Sat Nov 01 17:07:18 2025 +0000
@@ -0,0 +1,272 @@
+<?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 core-metrics" id="qiime2__boots__core_metrics" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Perform resampled "core metrics" analysis.</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 core_metrics '$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."/>
+        <repeat name="metadata" min="1" help="[required]  The sample metadata used in generating Emperor plots." title="metadata: Metadata">
+            <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                <param name="type" type="select" label="metadata: Metadata">
+                    <option value="tsv" selected="true">Metadata from TSV</option>
+                    <option value="qza">Metadata from Artifact</option>
+                </param>
+                <when value="tsv">
+                    <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
+                </when>
+                <when value="qza">
+                    <param name="source" type="data" format="qza" label="Metadata Source"/>
+                </when>
+            </conditional>
+        </repeat>
+        <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="alpha_average_method" type="select" label="alpha_average_method: Str % Choices('mean', 'median')" display="radio">
+                <option value="mean">mean</option>
+                <option value="median" selected="true">median</option>
+            </param>
+            <param name="beta_average_method" type="select" label="beta_average_method: Str % Choices('non-metric-mean', 'non-metric-median', 'medoid')" display="radio">
+                <option value="non-metric-mean">non-metric-mean</option>
+                <option value="non-metric-median" selected="true">non-metric-median</option>
+                <option value="medoid">medoid</option>
+            </param>
+            <param name="pc_dimensions" type="integer" value="3" label="pc_dimensions: Int" help="[default: 3]  Number of principal coordinate dimensions to present in the 2D scatterplot."/>
+            <conditional name="__q2galaxy__GUI__conditional__color_by__" label="color_by: Str">
+                <param name="__q2galaxy__GUI__select__" type="select" label="color_by: Str" help="[optional]  Categorical measure from the input Metadata that should be used for color-coding the 2D scatterplot.">
+                    <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
+                    <option value="__q2galaxy__::control::provide">Provide a value</option>
+                </param>
+                <when value="__q2galaxy__::control::default">
+                    <param name="color_by" type="hidden" value="__q2galaxy__::literal::None"/>
+                </when>
+                <when value="__q2galaxy__::control::provide">
+                    <param name="color_by" type="text">
+                        <sanitizer>
+                            <valid initial="string.printable"/>
+                        </sanitizer>
+                    </param>
+                </when>
+            </conditional>
+        </section>
+    </inputs>
+    <outputs>
+        <collection name="resampled_tables" type="list">
+            <discover_datasets directory="resampled_tables" pattern="__name_and_ext__"/>
+        </collection>
+        <collection name="alpha_diversities" type="list">
+            <discover_datasets directory="alpha_diversities" pattern="__name_and_ext__"/>
+        </collection>
+        <collection name="distance_matrices" type="list">
+            <discover_datasets directory="distance_matrices" pattern="__name_and_ext__"/>
+        </collection>
+        <collection name="pcoas" type="list">
+            <discover_datasets directory="pcoas" pattern="__name_and_ext__"/>
+        </collection>
+        <collection name="emperor_plots" type="list">
+            <discover_datasets directory="emperor_plots" pattern="__name_and_ext__"/>
+        </collection>
+        <data name="scatter_plot" format="qzv" label="${tool.name} on ${on_string}: scatter_plot.qzv" from_work_dir="scatter_plot.qzv"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="table" value="core_metrics.test0.table.qza" ftype="qza"/>
+            <param name="sampling_depth" value="20"/>
+            <repeat name="metadata">
+                <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                    <param name="type" value="tsv"/>
+                    <param name="source" value="core_metrics.test0.metadata.tsv" ftype="qiime2.tabular"/>
+                </conditional>
+            </repeat>
+            <param name="n" value="10"/>
+            <param name="replacement" value="__q2galaxy__::literal::True"/>
+            <param name="alpha_average_method" value="median"/>
+            <param name="beta_average_method" value="medoid"/>
+            <output_collection name="resampled_tables" type="list"/>
+            <output_collection name="alpha_diversities" type="list"/>
+            <output_collection name="distance_matrices" type="list"/>
+            <output_collection name="pcoas" type="list"/>
+            <output_collection name="emperor_plots" type="list"/>
+            <output name="scatter_plot" ftype="qzv"/>
+        </test>
+        <test>
+            <param name="table" value="core_metrics.test1.table.qza" ftype="qza"/>
+            <param name="sampling_depth" value="20"/>
+            <repeat name="metadata">
+                <conditional name="__q2galaxy__GUI__conditional__metadata__">
+                    <param name="type" value="tsv"/>
+                    <param name="source" value="core_metrics.test1.metadata.tsv" ftype="qiime2.tabular"/>
+                </conditional>
+            </repeat>
+            <param name="n" value="10"/>
+            <param name="replacement" value="__q2galaxy__::literal::False"/>
+            <param name="alpha_average_method" value="median"/>
+            <param name="beta_average_method" value="medoid"/>
+            <output_collection name="resampled_tables" type="list"/>
+            <output_collection name="alpha_diversities" type="list"/>
+            <output_collection name="distance_matrices" type="list"/>
+            <output_collection name="pcoas" type="list"/>
+            <output_collection name="emperor_plots" type="list"/>
+            <output name="scatter_plot" ftype="qzv"/>
+        </test>
+    </tests>
+    <help>
+QIIME 2: boots core-metrics
+===========================
+Perform resampled "core metrics" analysis.
+
+
+Outputs:
+--------
+:resampled_tables.qza: The `n` resampled tables.
+:alpha_diversities.qza: Average alpha diversity vector for each metric.
+:distance_matrices.qza: Average beta diversity distance matrix for each metric.
+:pcoas.qza: PCoA matrix for each beta diversity metric.
+:emperor_plots.qzv: Emperor plot for each beta diversity metric.
+:scatter_plot.qzv: 2D scatter plot including alpha diversity and pcoa results for all selected metrics.
+
+|  
+
+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 common alpha and beta diversity on each resulting `table`. The resulting artifacts are then averaged using the method specified by `alpha_average_method` and `beta_average_method` parameters. The resulting average alpha and beta diversity artifacts are returned, along with PCoA matrices, Emperor plots, and a 2D scatter plot including alpha diversity values and PCoA of all beta diversity metrics.
+
+Examples:
+---------
+
+Bootstrapped core metrics.
+**************************
+Using the ``qiime2 boots core-metrics`` tool:
+ #. Set *"table"* to ``#: table.qza``
+ #. Set *"sampling_depth"* to ``20``
+ #. For *"metadata"*:
+
+    - Perform the following steps.
+
+      #. Leave as ``Metadata from TSV``
+      #. Set *"Metadata Source"* to ``metadata.tsv``
+
+
+ #. Set *"n"* to ``10``
+ #. Set *"replacement"* to ``Yes``
+ #. Expand the ``additional options`` section
+
+    #. Leave *"alpha_average_method"* as its default value of ``median``
+    #. Set *"beta_average_method"* to ``medoid``
+
+ #. Press the ``Execute`` button.
+
+Once completed, for each 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 core-metrics [...] : resampled_tables.qza``
+      - ``bootstrap-tables/``
+    * - ``#: qiime2 boots core-metrics [...] : alpha_diversities.qza``
+      - ``bootstrap-alpha-diversities/``
+    * - ``#: qiime2 boots core-metrics [...] : distance_matrices.qza``
+      - ``bootstrap-distance-matrices/``
+    * - ``#: qiime2 boots core-metrics [...] : pcoas.qza``
+      - ``bootstrap-pcoas/``
+    * - ``#: qiime2 boots core-metrics [...] : emperor_plots.qza``
+      - ``bootstrap-emperor-plots/``
+    * - ``#: qiime2 boots core-metrics [...] : scatter_plot.qzv``
+      - ``scatter-plot.qzv``
+
+Rarefaction-based core metrics.
+*******************************
+Using the ``qiime2 boots core-metrics`` tool:
+ #. Set *"table"* to ``#: table.qza``
+ #. Set *"sampling_depth"* to ``20``
+ #. For *"metadata"*:
+
+    - Perform the following steps.
+
+      #. Leave as ``Metadata from TSV``
+      #. Set *"Metadata Source"* to ``metadata.tsv``
+
+
+ #. Set *"n"* to ``10``
+ #. Set *"replacement"* to ``No``
+ #. Expand the ``additional options`` section
+
+    #. Leave *"alpha_average_method"* as its default value of ``median``
+    #. Set *"beta_average_method"* to ``medoid``
+
+ #. Press the ``Execute`` button.
+
+Once completed, for each 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 core-metrics [...] : resampled_tables.qza``
+      - ``rarefaction-tables/``
+    * - ``#: qiime2 boots core-metrics [...] : alpha_diversities.qza``
+      - ``rarefaction-alpha-diversities/``
+    * - ``#: qiime2 boots core-metrics [...] : distance_matrices.qza``
+      - ``rarefaction-distance-matrices/``
+    * - ``#: qiime2 boots core-metrics [...] : pcoas.qza``
+      - ``rarefaction-pcoas/``
+    * - ``#: qiime2 boots core-metrics [...] : emperor_plots.qza``
+      - ``rarefaction-emperor-plots/``
+    * - ``#: qiime2 boots core-metrics [...] : scatter_plot.qzv``
+      - ``scatter-plot.qzv``
+
+
+|  
+
+</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 75593c55ca60 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 17:07:18 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 75593c55ca60 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 17:07:18 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 75593c55ca60 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 17:07:18 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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