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author | q2d2 |
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date | Mon, 29 Aug 2022 19:43:21 +0000 |
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<?xml version='1.0' encoding='utf-8'?> <!-- Copyright (c) 2022, 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: 2022.8.1) for: qiime2 (version: 2022.8.1) --> <tool name="qiime2 diversity-lib pielou-evenness" id="qiime2__diversity_lib__pielou_evenness" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> <description>Pielou's Evenness</description> <requirements> <container type="docker">quay.io/qiime2/core:2022.8</container> </requirements> <version_command>q2galaxy version diversity_lib</version_command> <command detect_errors="aggressive">q2galaxy run diversity_lib pielou_evenness '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> <inputs> <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency | RelativeFrequency]" help="[required] The feature table containing the samples for which Pielou's evenness should be computed."> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureTable[Frequency]"/> <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[RelativeFrequency]']</validator> </param> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> <param name="drop_undefined_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="drop_undefined_samples: Bool" help="[default: No] Samples with fewer than two observed features produce undefined (NaN) values. If true, these samples are dropped from the output vector."/> </section> </inputs> <outputs> <data name="vector" format="qza" label="${tool.name} on ${on_string}: vector.qza" from_work_dir="vector.qza"/> </outputs> <tests> <test> <param name="table" value="pielou_evenness.test0.feature-table.qza" ftype="qza"/> <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="pielou_evenness.test1.feature-table.qza" ftype="qza"/> <param name="drop_undefined_samples" value="__q2galaxy__::literal::True"/> <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> </tests> <help> QIIME 2: diversity-lib pielou-evenness ====================================== Pielou's Evenness Outputs: -------- :vector.qza: Vector containing per-sample values for Pielou's Evenness. | Description: ------------ Compute Pielou's Evenness for each sample in a feature table Examples: --------- basic ***** Using the ``qiime2 diversity-lib pielou-evenness`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. 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 pielou-evenness [...] : vector.qza`` - ``pielou-vector.qza`` dropping undefined samples ************************** Using the ``qiime2 diversity-lib pielou-evenness`` tool: #. Set *"table"* to ``#: feature-table.qza`` #. Expand the ``additional options`` section - Set *"drop_undefined_samples"* 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 diversity-lib pielou-evenness [...] : vector.qza`` - ``pielou-vector.qza`` | </help> <citations> <citation type="doi">10.1016/0022-5193(66)90013-0</citation> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>