Mercurial > repos > q2d2 > qiime2__diversity_lib__pielou_evenness
changeset 0:99b04636e7b5 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__diversity_lib commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__diversity_lib__pielou_evenness.xml Mon Aug 29 19:43:21 2022 +0000 @@ -0,0 +1,128 @@ +<?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>