# HG changeset patch
# User q2d2
# Date 1762017386 0
# Node ID 9e06bb95cbc41e6a957a03a112580d760d9bc675
# Parent  c80939f5905d63f3b01eeeb2dd2bab77e6743d5d
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b

diff -r c80939f5905d -r 9e06bb95cbc4 qiime2__diversity_lib__shannon_entropy.xml
--- a/qiime2__diversity_lib__shannon_entropy.xml	Tue Jul 15 21:53:45 2025 +0000
+++ b/qiime2__diversity_lib__shannon_entropy.xml	Sat Nov 01 17:16:26 2025 +0000
@@ -6,17 +6,17 @@
 -->
 <!--
 This tool was automatically generated by:
-    q2galaxy (version: 2025.7.0)
+    q2galaxy (version: 2025.10.0)
 for:
-    qiime2 (version: 2025.7.0)
+    qiime2 (version: 2025.10.0)
 -->
-<tool name="qiime2 diversity-lib shannon-entropy" id="qiime2__diversity_lib__shannon_entropy" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause">
+<tool name="qiime2 diversity-lib shannon-entropy" id="qiime2__diversity_lib__shannon_entropy" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause">
     <description>Shannon's Entropy</description>
     <xrefs>
         <xref type="bio.tools">qiime2</xref>
     </xrefs>
     <requirements>
-        <container type="docker">quay.io/qiime2/amplicon:2025.7</container>
+        <container type="docker">quay.io/qiime2/amplicon:2025.10</container>
     </requirements>
     <version_command>q2galaxy version diversity_lib</version_command>
     <command detect_errors="exit_code">q2galaxy run diversity_lib shannon_entropy '$inputs'</command>
@@ -26,13 +26,25 @@
     <inputs>
         <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required]  The feature table containing the samples for which Shannon's Entropy should be computed.">
             <options options_filter_attribute="metadata.semantic_type">
+                <filter type="add_value" value="FeatureTable[Frequency]"/>
                 <filter type="add_value" value="FeatureTable[RelativeFrequency]"/>
-                <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]', 'FeatureTable[RelativeFrequency]']</validator>
         </param>
         <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
             <param name="drop_undefined_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="drop_undefined_samples: Bool" help="[default: No]  Samples with no observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector."/>
+            <conditional name="__q2galaxy__GUI__conditional__base__">
+                <param name="__q2galaxy__GUI__select__" type="select" label="base: Float % Range(0, None, inclusive_start=False) | Str % Choices('e')" help="[default: 2]  The logarithm base used in calculations.">
+                    <option value="e">e (Str)</option>
+                    <option value="__q2galaxy__::control::Float X Range(0__comma__ None__comma__ inclusive_start=False)" selected="true">Provide a value (Float % Range(0, None, inclusive_start=False))</option>
+                </param>
+                <when value="e">
+                    <param name="base" type="hidden" value="e"/>
+                </when>
+                <when value="__q2galaxy__::control::Float X Range(0__comma__ None__comma__ inclusive_start=False)">
+                    <param name="base" type="float" min="1e-06" value="2" label="base: Float % Range(0, None, inclusive_start=False)" help="[default: 2]  The logarithm base used in calculations."/>
+                </when>
+            </conditional>
         </section>
     </inputs>
     <outputs>
@@ -51,6 +63,20 @@
         </test>
         <test>
             <param name="table" value="shannon_entropy.test1.feature-table.qza" ftype="qza"/>
+            <conditional name="__q2galaxy__GUI__conditional__base__">
+                <param name="__q2galaxy__GUI__select__" value="e"/>
+                <param name="base" value="e"/>
+            </conditional>
+            <output name="vector" ftype="qza">
+                <assert_contents>
+                    <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml">
+                        <has_line_matching expression="type: SampleData\[AlphaDiversity\]"/>
+                    </has_archive_member>
+                </assert_contents>
+            </output>
+        </test>
+        <test>
+            <param name="table" value="shannon_entropy.test2.feature-table.qza" ftype="qza"/>
             <param name="drop_undefined_samples" value="__q2galaxy__::literal::True"/>
             <output name="vector" ftype="qza">
                 <assert_contents>
@@ -98,6 +124,31 @@
     * - ``#: qiime2 diversity-lib shannon-entropy [...] : vector.qza``
       - ``shannon-vector.qza``
 
+base_e
+******
+| Set the logarithm base to e for the Shannon calculation. 
+| This will result in values that match those produced by 
+| vegan and scikit-bio.
+Using the ``qiime2 diversity-lib shannon-entropy`` tool:
+ #. Set *"table"* to ``#: feature-table.qza``
+ #. Expand the ``additional options`` section
+
+    - Set *"base"* to ``e``
+
+ #. 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 diversity-lib shannon-entropy [...] : vector.qza``
+      - ``shannon-vector.qza``
+
 dropping undefined samples
 **************************
 Using the ``qiime2 diversity-lib shannon-entropy`` tool:
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/alpha_passthrough.test0.feature-table.qza
Binary file test-data/alpha_passthrough.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_passthrough.test0.feature-table.qza
Binary file test-data/beta_passthrough.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_passthrough.test1.feature-table.qza
Binary file test-data/beta_passthrough.test1.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_passthrough.test2.feature-table.qza
Binary file test-data/beta_passthrough.test2.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_passthrough.test3.feature-table.qza
Binary file test-data/beta_passthrough.test3.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test0.feature-table1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.feature-table1.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test0.feature-table2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.feature-table2.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny1.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test0.phylogeny2.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test1.feature-table1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test1.feature-table1.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test1.feature-table2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test1.feature-table2.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test1.phylogeny.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test1.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test2.feature-table1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.feature-table1.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test2.feature-table2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.feature-table2.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny1.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny1.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny2.qza
Binary file test-data/beta_phylogenetic_meta_passthrough.test2.phylogeny2.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test0.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test0.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test0.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test1.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test1.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test1.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test1.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test2.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test2.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test2.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test2.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test3.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test3.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test3.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test3.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test4.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test4.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test4.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test4.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test5.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test5.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test5.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test5.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test6.feature-table.qza
Binary file test-data/beta_phylogenetic_passthrough.test6.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/beta_phylogenetic_passthrough.test6.phylogeny.qza
Binary file test-data/beta_phylogenetic_passthrough.test6.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/bray_curtis.test0.feature-table.qza
Binary file test-data/bray_curtis.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/bray_curtis.test1.feature-table.qza
Binary file test-data/bray_curtis.test1.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/bray_curtis.test2.feature-table.qza
Binary file test-data/bray_curtis.test2.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/faith_pd.test0.feature-table.qza
Binary file test-data/faith_pd.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/faith_pd.test0.phylogeny.qza
Binary file test-data/faith_pd.test0.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/jaccard.test0.feature-table.qza
Binary file test-data/jaccard.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/jaccard.test1.feature-table.qza
Binary file test-data/jaccard.test1.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/jaccard.test2.feature-table.qza
Binary file test-data/jaccard.test2.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/observed_features.test0.feature-table.qza
Binary file test-data/observed_features.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/pielou_evenness.test0.feature-table.qza
Binary file test-data/pielou_evenness.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/pielou_evenness.test1.feature-table.qza
Binary file test-data/pielou_evenness.test1.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/shannon_entropy.test0.feature-table.qza
Binary file test-data/shannon_entropy.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/shannon_entropy.test1.feature-table.qza
Binary file test-data/shannon_entropy.test1.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/shannon_entropy.test2.feature-table.qza
Binary file test-data/shannon_entropy.test2.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/unweighted_unifrac.test0.feature-table.qza
Binary file test-data/unweighted_unifrac.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/unweighted_unifrac.test0.phylogeny.qza
Binary file test-data/unweighted_unifrac.test0.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/unweighted_unifrac.test1.feature-table.qza
Binary file test-data/unweighted_unifrac.test1.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/unweighted_unifrac.test1.phylogeny.qza
Binary file test-data/unweighted_unifrac.test1.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/unweighted_unifrac.test2.feature-table.qza
Binary file test-data/unweighted_unifrac.test2.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/unweighted_unifrac.test2.phylogeny.qza
Binary file test-data/unweighted_unifrac.test2.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/unweighted_unifrac.test3.feature-table.qza
Binary file test-data/unweighted_unifrac.test3.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/unweighted_unifrac.test3.phylogeny.qza
Binary file test-data/unweighted_unifrac.test3.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/weighted_unifrac.test0.feature-table.qza
Binary file test-data/weighted_unifrac.test0.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/weighted_unifrac.test0.phylogeny.qza
Binary file test-data/weighted_unifrac.test0.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/weighted_unifrac.test1.feature-table.qza
Binary file test-data/weighted_unifrac.test1.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/weighted_unifrac.test1.phylogeny.qza
Binary file test-data/weighted_unifrac.test1.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/weighted_unifrac.test2.feature-table.qza
Binary file test-data/weighted_unifrac.test2.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/weighted_unifrac.test2.phylogeny.qza
Binary file test-data/weighted_unifrac.test2.phylogeny.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/weighted_unifrac.test3.feature-table.qza
Binary file test-data/weighted_unifrac.test3.feature-table.qza has changed
diff -r c80939f5905d -r 9e06bb95cbc4 test-data/weighted_unifrac.test3.phylogeny.qza
Binary file test-data/weighted_unifrac.test3.phylogeny.qza has changed