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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 17:08:11 +0000
parents
children
files qiime2__boots__resample.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, 150 insertions(+), 0 deletions(-) [+]
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__boots__resample.xml	Sat Nov 01 17:08:11 2025 +0000
@@ -0,0 +1,132 @@
+<?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 resample" id="qiime2__boots__resample" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
+    <description>Resample feature table, returning `n` feature tables.</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 resample '$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]" help="[required]  The input feature table.">
+            <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
+            </options>
+            <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</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>
+    </inputs>
+    <outputs>
+        <collection name="resampled_tables" type="list">
+            <discover_datasets directory="resampled_tables" pattern="__name_and_ext__"/>
+        </collection>
+    </outputs>
+    <tests>
+        <test>
+            <param name="table" value="resample.test0.table.qza" ftype="qza"/>
+            <param name="sampling_depth" value="20"/>
+            <param name="n" value="10"/>
+            <param name="replacement" value="__q2galaxy__::literal::True"/>
+            <output_collection name="resampled_tables" type="list"/>
+        </test>
+        <test>
+            <param name="table" value="resample.test1.table.qza" ftype="qza"/>
+            <param name="sampling_depth" value="20"/>
+            <param name="n" value="10"/>
+            <param name="replacement" value="__q2galaxy__::literal::False"/>
+            <output_collection name="resampled_tables" type="list"/>
+        </test>
+    </tests>
+    <help>
+QIIME 2: boots resample
+=======================
+Resample feature table, returning `n` feature tables.
+
+
+Outputs:
+--------
+:resampled_tables.qza: The `n` resampled tables.
+
+|  
+
+Description:
+------------
+Resample `table` to `sampling_depth` total observations with replacement (i.e., bootstrapping) or without replacement (i.e., rarefaction) `n` times, to generate `n` resampled feature tables.
+
+Examples:
+---------
+
+Generate 10 bootstrapped tables.
+********************************
+Using the ``qiime2 boots resample`` tool:
+ #. Set *"table"* to ``#: table.qza``
+ #. Set *"sampling_depth"* to ``20``
+ #. Set *"n"* to ``10``
+ #. Set *"replacement"* to ``Yes``
+ #. 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 resample [...] : resampled_tables.qza``
+      - ``bootstrapped-tables/``
+
+Generate 10 rarefied tables.
+****************************
+Using the ``qiime2 boots resample`` tool:
+ #. Set *"table"* to ``#: table.qza``
+ #. Set *"sampling_depth"* to ``20``
+ #. Set *"n"* to ``10``
+ #. Set *"replacement"* to ``No``
+ #. 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 resample [...] : resampled_tables.qza``
+      - ``rarefaction-tables/``
+
+
+|  
+
+</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>
Binary file test-data/alpha.test0.table.qza has changed
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/core_metrics.test0.metadata.tsv	Sat Nov 01 17:08:11 2025 +0000
@@ -0,0 +1,6 @@
+sample-id	even-or-odd
+#q2:types	categorical
+S1	odd
+S2	even
+S3	odd
+S4	even
Binary file test-data/core_metrics.test0.table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/core_metrics.test1.metadata.tsv	Sat Nov 01 17:08:11 2025 +0000
@@ -0,0 +1,6 @@
+sample-id	even-or-odd
+#q2:types	categorical
+S1	odd
+S2	even
+S3	odd
+S4	even
Binary file test-data/core_metrics.test1.table.qza has changed
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/kmer_diversity.test0.metadata.tsv	Sat Nov 01 17:08:11 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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Binary file test-data/kmer_diversity.test0.table.qza has changed
Binary file test-data/resample.test0.table.qza has changed
Binary file test-data/resample.test1.table.qza has changed