Mercurial > repos > q2d2 > qiime2__feature_table__rename_ids
changeset 0:5e6afe86c5b8 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 19:59:34 +0000 |
| parents | |
| children | d473dc9e00e2 |
| files | qiime2__feature_table__rename_ids.xml test-data/merge.test0.feature-table1.qza test-data/merge.test0.feature-table2.qza test-data/merge.test1.feature-table1.qza test-data/merge.test1.feature-table2.qza test-data/merge.test1.feature-table3.qza |
| diffstat | 6 files changed, 86 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__feature_table__rename_ids.xml Mon Aug 29 19:59:34 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 feature-table rename-ids" id="qiime2__feature_table__rename_ids" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Renames sample or feature ids in a table</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version feature_table</version_command> + <command detect_errors="aggressive">q2galaxy run feature_table rename_ids '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The table to be renamed"> + <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> + <conditional name="metadata"> + <param name="type" type="select" label="metadata: MetadataColumn[Categorical]" help="[required] A metadata column defining the new ids. Each original id must map to a new unique id. If strict mode is used, then every id in the original table must have a new id."> + <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"/> + <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true"> + <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator> + </param> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + <param name="column" type="text" label="Column Name"> + <validator type="empty_field"/> + </param> + </when> + </conditional> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="axis" type="select" label="axis: Str % Choices('feature', 'sample')" display="radio"> + <option value="feature">feature</option> + <option value="sample" selected="true">sample</option> + </param> + <param name="strict" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="strict: Bool" help="[default: No] Whether the naming needs to be strict (each id in the table must have a new id). Otherwise, only the ids described in `metadata` will be renamed and the others will keep their original id names."/> + </section> + </inputs> + <outputs> + <data name="renamed_table" format="qza" label="${tool.name} on ${on_string}: renamed_table.qza" from_work_dir="renamed_table.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: feature-table rename-ids +================================= +Renames sample or feature ids in a table + + +Outputs: +-------- +:renamed_table.qza: A table which has new ids, where the ids are replaced by values in the `metadata` column. + +| + +Description: +------------ +Renames the sample or feature ids in a feature table using metadata to define the new ids. + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>