Mercurial > repos > q2d2 > qiime2__phylogeny__filter_table
changeset 0:fce718a0b52f draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__phylogeny commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 20:14:41 +0000 |
| parents | |
| children | 63f054c1fce2 |
| files | qiime2__phylogeny__filter_table.xml test-data/.gitkeep |
| diffstat | 1 files changed, 67 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__phylogeny__filter_table.xml Mon Aug 29 20:14:41 2022 +0000 @@ -0,0 +1,67 @@ +<?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-table" id="qiime2__phylogeny__filter_table" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Remove features from table if they're not present in tree.</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_table '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³]" help="[required] Feature table that features should be filtered from."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> + <filter type="add_value" value="FeatureTable[Frequency]"/> + <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> + </param> + <param name="tree" type="data" format="qza" label="tree: Phylogeny[Rooted | Unrooted]" help="[required] Tree where tip identifiers are the feature identifiers that should be retained in the table."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="Phylogeny[Unrooted]"/> + <filter type="add_value" value="Phylogeny[Rooted]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['Phylogeny[Rooted]', 'Phylogeny[Unrooted]']</validator> + </param> + </inputs> + <outputs> + <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: phylogeny filter-table +=============================== +Remove features from table if they're not present in tree. + + +Outputs: +-------- +:filtered_table.qza: The resulting feature table. + +| + +Description: +------------ +Remove features from a feature table if their identifiers are not tip identifiers in tree. + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>