Mercurial > repos > q2d2 > qiime2__emperor__plot
changeset 0:e6978c621d70 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 19:49:22 +0000 |
parents | |
children | 7c9ec8b8b7f8 |
files | qiime2__emperor__plot.xml test-data/.gitkeep |
diffstat | 1 files changed, 86 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__emperor__plot.xml Mon Aug 29 19:49:22 2022 +0000 @@ -0,0 +1,86 @@ +<?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 emperor plot" id="qiime2__emperor__plot" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Visualize and Interact with Principal Coordinates Analysis Plots</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version emperor</version_command> + <command detect_errors="aggressive">q2galaxy run emperor plot '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="pcoa" type="data" format="qza" label="pcoa: PCoAResults" help="[required] The principal coordinates matrix to be plotted."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="PCoAResults"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['PCoAResults']</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> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <repeat name="custom_axes" help="[optional] Numeric sample metadata columns that should be included as axes in the Emperor plot." title="custom_axes: 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="ignore_missing_samples" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_missing_samples: Bool" help="[default: No] This will suppress the error raised when the coordinates matrix contains samples that are not present in the metadata. Samples without metadata are included by setting all metadata values to: "This sample has no metadata". This flag is only applied if at least one sample is present in both the coordinates matrix and the metadata."/> + <param name="ignore_pcoa_features" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="ignore_pcoa_features: Bool" help="[default: No] Biplot arrows cannot be visualized using this method. If you want to visualize biplot arrows use the `biplot` method. Enabling this setting will ignore any PCoA features that are present, otherwise, if PCoA features are detected an error will be raised."/> + </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: emperor plot +===================== +Visualize and Interact with Principal Coordinates Analysis Plots + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Generates an interactive ordination plot where the user can visually integrate sample metadata. + + +| + +</help> + <citations> + <citation type="doi">10.1186/2047-217X-2-16</citation> + <citation type="doi">10.1016/j.chom.2016.12.009</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>