| Next changeset 1:bd0dbc487394 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__emperor commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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added:
qiime2__emperor__procrustes_plot.xml test-data/.gitkeep |
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| diff -r 000000000000 -r 7c4129b3c5ea qiime2__emperor__procrustes_plot.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__emperor__procrustes_plot.xml Mon Aug 29 19:48:36 2022 +0000 |
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| @@ -0,0 +1,97 @@ +<?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 procrustes-plot" id="qiime2__emperor__procrustes_plot" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Visualize and Interact with a procrustes plot</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 procrustes_plot '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="reference_pcoa" type="data" format="qza" label="reference_pcoa: PCoAResults" help="[required] The reference ordination 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> + <param name="other_pcoa" type="data" format="qza" label="other_pcoa: PCoAResults" help="[required] The "other" ordination matrix to be plotted (the one that was fitted to the reference)."> + <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"> + <param name="m2_stats" type="data" format="qza" optional="true" label="m2_stats: ProcrustesStatistics" help="[optional] The M^2 value of the procrustes analysis & its associated p value."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="ProcrustesStatistics"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['ProcrustesStatistics']</validator> + </param> + <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."/> + </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 procrustes-plot +================================ +Visualize and Interact with a procrustes plot + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Plot two procrustes-fitted matrices + + +| + +</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> |