Mercurial > repos > q2d2 > qiime2__longitudinal__volatility
changeset 0:55fd8d766006 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__longitudinal commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 20:10:48 +0000 |
| parents | |
| children | bea0cdf2d9c8 |
| files | qiime2__longitudinal__volatility.xml test-data/.gitkeep |
| diffstat | 1 files changed, 135 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__longitudinal__volatility.xml Mon Aug 29 20:10:48 2022 +0000 @@ -0,0 +1,135 @@ +<?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 longitudinal volatility" id="qiime2__longitudinal__volatility" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Generate interactive volatility plot</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version longitudinal</version_command> + <command detect_errors="aggressive">q2galaxy run longitudinal volatility '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <repeat name="metadata" min="1" help="[required] Sample metadata file containing individual_id_column." 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="state_column" type="text" label="state_column: Str" help="[required] Metadata column containing state (time) variable information."> + <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="table" type="data" format="qza" optional="true" label="table: FeatureTable[RelativeFrequency]" help="[optional] Feature table containing metrics."> + <options options_filter_attribute="metadata.semantic_type"> + <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[RelativeFrequency]']</validator> + </param> + <conditional name="__q2galaxy__GUI__conditional__individual_id_column__" label="individual_id_column: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="individual_id_column: Str" help="[optional] Metadata column containing IDs for individual subjects."> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="individual_id_column" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="individual_id_column" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <conditional name="__q2galaxy__GUI__conditional__default_group_column__" label="default_group_column: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="default_group_column: Str" help="[optional] The default metadata column on which to separate groups for comparison (all categorical metadata columns will be available in the visualization)."> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="default_group_column" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="default_group_column" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <conditional name="__q2galaxy__GUI__conditional__default_metric__" label="default_metric: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="default_metric: Str" help="[optional] Numeric metadata or artifact column to test by default (all numeric metadata columns will be available in the visualization)."> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="default_metric" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="default_metric" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <param name="yscale" type="select" label="yscale: Str % Choices('linear', 'pow', 'sqrt', 'log')" display="radio"> + <option value="linear" selected="true">linear</option> + <option value="pow">pow</option> + <option value="sqrt">sqrt</option> + <option value="log">log</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: longitudinal volatility +================================ +Generate interactive volatility plot + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Generate an interactive control chart depicting the longitudinal volatility of sample metadata and/or feature frequencies across time (as set using the "state_column" parameter). Any numeric metadata column (and metadata-transformable artifacts, e.g., alpha diversity results) can be plotted on the y-axis, and are selectable using the "metric_column" selector. Metric values are averaged to compare across any categorical metadata column using the "group_column" selector. Longitudinal volatility for individual subjects sampled over time is co-plotted as "spaghetti" plots if the "individual_id_column" parameter is used. state_column will typically be a measure of time, but any numeric metadata column can be used. + + +| + +</help> + <citations> + <citation type="doi">10.1128/mSystems.00219-18</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>