Mercurial > repos > q2d2 > qiime2__composition__ancombc
diff qiime2__composition__ancombc.xml @ 0:9b2a68d3017f draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 69da7976573cc07a363ac66bdacc9269d7cd3732
| author | q2d2 |
|---|---|
| date | Fri, 13 Jan 2023 22:04:42 +0000 |
| parents | |
| children | fe99db171ce5 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__composition__ancombc.xml Fri Jan 13 22:04:42 2023 +0000 @@ -0,0 +1,209 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2023, 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: 2022.11.1) +for: + qiime2 (version: 2022.11.1) +--> +<tool name="qiime2 composition ancombc" id="qiime2__composition__ancombc" version="2022.11.2+q2galaxy.2022.11.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Analysis of Composition of Microbiomes with Bias Correction</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.11</container> + </requirements> + <version_command>q2galaxy version composition</version_command> + <command detect_errors="exit_code">q2galaxy run composition ancombc '$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 to be used for ANCOM computation."> + <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> + <repeat name="metadata" min="1" help="[required] The sample metadata." title="metadata: Metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" type="select" label="metadata: Metadata"> + <option value="tsv" selected="true">Metadata from TSV</option> + <option value="qza">Metadata from Artifact</option> + </param> + <when value="tsv"> + <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + </when> + </conditional> + </repeat> + <param name="formula" type="text" label="formula: Str" help="[required] How the microbial absolute abundances for each taxon depend on the variables within the `metadata`."> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="p_adj_method" type="select" label="p_adj_method: Str % Choices('holm', 'hochberg', 'hommel', 'bonferroni', 'BH', 'BY', 'fdr', 'none')"> + <option value="holm" selected="true">holm</option> + <option value="hochberg">hochberg</option> + <option value="hommel">hommel</option> + <option value="bonferroni">bonferroni</option> + <option value="BH">BH</option> + <option value="BY">BY</option> + <option value="fdr">fdr</option> + <option value="none">none</option> + </param> + <param name="prv_cut" type="float" value="0.1" label="prv_cut: Float" help="[default: 0.1] A numerical fraction between 0-1. Taxa with prevalences less than this value will be excluded from the analysis."/> + <param name="lib_cut" type="integer" value="0" label="lib_cut: Int" help="[default: 0] A numerical threshold for filtering samples based on library sizes. Samples with library sizes less than this value will be excluded from the analysis."/> + <repeat name="reference_levels" help="[optional] Define the reference level(s) to be used for categorical columns found in the `formula`. These categorical factors are dummy coded relative to the reference(s) provided. The syntax is as follows: "column_name::column_value"" title="reference_levels: List[Str]"> + <param name="element" type="text" label="element: Str" help="[required]"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + </repeat> + <param name="neg_lb" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="neg_lb: Bool" help="[default: No] Whether to classify a taxon as a structural zero using its asymptotic lower bound."/> + <param name="tol" type="float" value="1e-05" label="tol: Float" help="[default: 1e-05] The iteration convergence tolerance for the E-M algorithm."/> + <param name="max_iter" type="integer" value="100" label="max_iter: Int" help="[default: 100] The maximum number of iterations for the E-M algorithm."/> + <param name="conserve" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="conserve: Bool" help="[default: No] Whether to use a conservative variance estimator for the test statistic. It is recommended if the sample size is small and/or the number of differentially abundant taxa is believed to be large."/> + <param name="alpha" type="float" value="0.05" label="alpha: Float" help="[default: 0.05] Level of significance."/> + </section> + </inputs> + <outputs> + <data name="differentials" format="qza" label="${tool.name} on ${on_string}: differentials.qza" from_work_dir="differentials.qza"/> + </outputs> + <tests> + <test> + <param name="table" value="ancombc.test0.table.qza" ftype="qza"/> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="ancombc.test0.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <param name="formula" value="bodysite"/> + <output name="differentials" 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: FeatureData\[DifferentialAbundance\]"/> + </has_archive_member> + </assert_contents> + </output> + </test> + <test> + <param name="table" value="ancombc.test1.table.qza" ftype="qza"/> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="tsv"/> + <param name="source" value="ancombc.test1.metadata.tsv" ftype="qiime2.tabular"/> + </conditional> + </repeat> + <param name="formula" value="bodysite + month"/> + <repeat name="reference_levels"> + <param name="element" value="bodysite::tongue"/> + </repeat> + <output name="differentials" 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: FeatureData\[DifferentialAbundance\]"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> + <help> +QIIME 2: composition ancombc +============================ +Analysis of Composition of Microbiomes with Bias Correction + + +Outputs: +-------- +:differentials.qza: The calculated per-feature differentials. + +| + +Description: +------------ +ANCOM-BC description goes here. + +Examples: +--------- + +ancombc_single_formula +********************** +Using the ``qiime2 composition ancombc`` tool: + #. Set *"table"* to ``#: table.qza`` + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"formula"* to ``bodysite`` + #. 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 composition ancombc [...] : differentials.qza`` + - ``dataloaf.qza`` + +ancombc_multi_formula_with_reference_levels +******************************************* +Using the ``qiime2 composition ancombc`` tool: + #. Set *"table"* to ``#: table.qza`` + #. For *"metadata"*: + + - Perform the following steps. + + #. Leave as ``Metadata from TSV`` + #. Set *"Metadata Source"* to ``metadata.tsv`` + + + #. Set *"formula"* to ``bodysite + month`` + #. Expand the ``additional options`` section + + - For *"reference_levels"*: + + #. Set *"element"* to ``bodysite::tongue`` + #. (Do not insert additional values.) + + + #. 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 composition ancombc [...] : differentials.qza`` + - ``dataloaf.qza`` + + +| + +</help> + <citations> + <citation type="doi">10.3402/mehd.v26.27663</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>