Mercurial > repos > q2d2 > qiime2__diversity_lib__alpha_passthrough
changeset 0:ad78836bc67b 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__alpha_passthrough.xml Mon Aug 29 19:41:15 2022 +0000 @@ -0,0 +1,122 @@ +<?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 alpha-passthrough" id="qiime2__diversity_lib__alpha_passthrough" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Alpha Passthrough (non-phylogenetic)</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 alpha_passthrough '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table containing the samples for which a selected metric should be computed."> + <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="metric" type="select" label="metric: Str % Choices('ace', 'berger_parker_d', 'brillouin_d', 'chao1', 'chao1_ci', 'dominance', 'doubles', 'enspie', 'esty_ci', 'fisher_alpha', 'gini_index', 'goods_coverage', 'heip_e', 'kempton_taylor_q', 'lladser_pe', 'margalef', 'mcintosh_d', 'mcintosh_e', 'menhinick', 'michaelis_menten_fit', 'osd', 'robbins', 'simpson', 'simpson_e', 'singles', 'strong')"> + <option value="__q2galaxy__::literal::None">Selection required</option> + <option value="ace">ace</option> + <option value="berger_parker_d">berger_parker_d</option> + <option value="brillouin_d">brillouin_d</option> + <option value="chao1">chao1</option> + <option value="chao1_ci">chao1_ci</option> + <option value="dominance">dominance</option> + <option value="doubles">doubles</option> + <option value="enspie">enspie</option> + <option value="esty_ci">esty_ci</option> + <option value="fisher_alpha">fisher_alpha</option> + <option value="gini_index">gini_index</option> + <option value="goods_coverage">goods_coverage</option> + <option value="heip_e">heip_e</option> + <option value="kempton_taylor_q">kempton_taylor_q</option> + <option value="lladser_pe">lladser_pe</option> + <option value="margalef">margalef</option> + <option value="mcintosh_d">mcintosh_d</option> + <option value="mcintosh_e">mcintosh_e</option> + <option value="menhinick">menhinick</option> + <option value="michaelis_menten_fit">michaelis_menten_fit</option> + <option value="osd">osd</option> + <option value="robbins">robbins</option> + <option value="simpson">simpson</option> + <option value="simpson_e">simpson_e</option> + <option value="singles">singles</option> + <option value="strong">strong</option> + <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> + </param> + </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="alpha_passthrough.test0.feature-table.qza" ftype="qza"/> + <param name="metric" value="simpson"/> + <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 alpha-passthrough +======================================== +Alpha Passthrough (non-phylogenetic) + + +Outputs: +-------- +:vector.qza: Vector containing per-sample values for the chosen metric. + +| + +Description: +------------ +Computes a vector of values (one value for each samples in a feature table) using the scikit-bio implementation of the selected alpha diversity metric. + +Examples: +--------- + +basic +***** +Using the ``qiime2 diversity-lib alpha-passthrough`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Set *"metric"* to ``simpson`` + #. 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 alpha-passthrough [...] : vector.qza`` + - ``simpson-vector.qza`` + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>