Mercurial > repos > q2d2 > qiime2__composition__ancom
changeset 0:cba57f5ca371 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__composition commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
---|---|
date | Mon, 29 Aug 2022 19:20:05 +0000 |
parents | |
children | 4696fc685d83 |
files | qiime2__composition__ancom.xml test-data/.gitkeep |
diffstat | 1 files changed, 89 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__composition__ancom.xml Mon Aug 29 19:20:05 2022 +0000 @@ -0,0 +1,89 @@ +<?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 composition ancom" id="qiime2__composition__ancom" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Apply ANCOM to identify features that differ in abundance.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version composition</version_command> + <command detect_errors="aggressive">q2galaxy run composition ancom '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="table" type="data" format="qza" label="table: FeatureTable[Composition]" help="[required] The feature table to be used for ANCOM computation."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[Composition]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]']</validator> + </param> + <conditional name="metadata"> + <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required] The categorical sample metadata column to test for differential abundance across."> + <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"/> + <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> + <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> + </param> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + <param name="column" type="text" label="Column Name"> + <validator type="empty_field"/> + </param> + </when> + </conditional> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="transform_function" type="select" label="transform_function: Str % Choices('sqrt', 'log', 'clr')" display="radio"> + <option value="sqrt">sqrt</option> + <option value="log">log</option> + <option value="clr" selected="true">clr</option> + </param> + <param name="difference_function" type="select" label="difference_function: Str % Choices('mean_difference', 'f_statistic')" display="radio"> + <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option> + <option value="mean_difference">mean_difference</option> + <option value="f_statistic">f_statistic</option> + </param> + </section> + </inputs> + <outputs> + <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> + </outputs> + <tests/> + <help> +QIIME 2: composition ancom +========================== +Apply ANCOM to identify features that differ in abundance. + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Apply Analysis of Composition of Microbiomes (ANCOM) to identify features that are differentially abundant across groups. + + +| + +</help> + <citations> + <citation type="doi">10.3402/mehd.v26.27663</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>