| Next changeset 1:2f35a9736467 (2023-01-13) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1 |
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added:
qiime2__phylogeny__filter_tree.xml test-data/.gitkeep |
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| diff -r 000000000000 -r fd4dc4e33218 qiime2__phylogeny__filter_tree.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__phylogeny__filter_tree.xml Mon Aug 29 20:15:54 2022 +0000 |
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| @@ -0,0 +1,100 @@ +<?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 phylogeny filter-tree" id="qiime2__phylogeny__filter_tree" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Remove features from tree based on metadata</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version phylogeny</version_command> + <command detect_errors="aggressive">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[Unrooted]"/> + <filter type="add_value" value="Phylogeny[Rooted]"/> + </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[Composition]"/> + <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> + <filter type="add_value" value="FeatureTable[Frequency]"/> + <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[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> |