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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 65e4952f33eb335528e8553150e9097e5ea8f556
author | q2d2 |
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date | Thu, 08 Jun 2023 19:49:48 +0000 |
parents | 2f35a9736467 |
children | fbdbfcbe5121 |
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<?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: 2023.5.0) for: qiime2 (version: 2023.5.1) --> <tool name="qiime2 phylogeny filter-tree" id="qiime2__phylogeny__filter_tree" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> <description>Remove features from tree based on metadata</description> <requirements> <container type="docker">quay.io/qiime2/core:2023.5</container> </requirements> <version_command>q2galaxy version phylogeny</version_command> <command detect_errors="exit_code">q2galaxy run phylogeny filter_tree '$inputs'</command> <configfiles> <inputs name="inputs" data_style="paths"/> </configfiles> <inputs> <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted¹ | Unrooted²]" help="[required] Tree that should be filtered"> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="Phylogeny[Rooted]"/> <filter type="add_value" value="Phylogeny[Unrooted]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]', 'Phylogeny[Unrooted]']</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[Frequency | RelativeFrequency | PresenceAbsence | Composition]" help="[optional] Feature table which contains the identifier that should be retained in the tree"> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureTable[Frequency]"/> <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> <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]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> </param> <repeat name="metadata" help="[optional] Feature metadata to use with the 'where' statement or to select tips to be retained. Metadata objects could also include FeatureData[Sequence] data types, if, forinstance, you want to filter to match represenative sequencces." 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> <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str"> <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional] SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered feature table. If not provided, all samples in `metadata` that are also in the feature table will be retained."> <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="where" type="hidden" value="__q2galaxy__::literal::None"/> </when> <when value="__q2galaxy__::control::provide"> <param name="where" type="text"> <sanitizer> <valid initial="string.printable"/> </sanitizer> </param> </when> </conditional> </section> </inputs> <outputs> <data name="filtered_tree" format="qza" label="${tool.name} on ${on_string}: filtered_tree.qza" from_work_dir="filtered_tree.qza"/> </outputs> <tests/> <help> QIIME 2: phylogeny filter-tree ============================== Remove features from tree based on metadata Outputs: -------- :filtered_tree.qza: The resulting phylogenetic tree. | Description: ------------ Remove tips from a tree if their identifiers based on a set of provided identifiers. | </help> <citations> <citation type="doi">10.1038/s41587-019-0209-9</citation> </citations> </tool>