Mercurial > repos > q2d2 > qiime2__diversity_lib__shannon_entropy
changeset 8:9e06bb95cbc4 draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b
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--- 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: