Mercurial > repos > q2d2 > qiime2__feature_table__rarefy
changeset 0:c234fbc63b48 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 20:01:16 +0000 |
| parents | |
| children | 985c7f96ce2a |
| files | qiime2__feature_table__rarefy.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, 63 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__feature_table__rarefy.xml Mon Aug 29 20:01:16 2022 +0000 @@ -0,0 +1,63 @@ +<?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 rarefy" id="qiime2__feature_table__rarefy" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Rarefy 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 rarefy '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table to be rarefied."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[Frequency]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> + </param> + <param name="sampling_depth" type="integer" min="1" value="" label="sampling_depth: Int % Range(1, None)" help="[required] The total frequency that each sample should be rarefied to. Samples where the sum of frequencies is less than the sampling depth will be not be included in the resulting table unless subsampling is performed with replacement."/> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="with_replacement" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="with_replacement: Bool" help="[default: No] Rarefy with replacement by sampling from the multinomial distribution instead of rarefying without replacement."/> + </section> + </inputs> + <outputs> + <data name="rarefied_table" format="qza" label="${tool.name} on ${on_string}: rarefied_table.qza" from_work_dir="rarefied_table.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: feature-table rarefy +============================= +Rarefy table + + +Outputs: +-------- +:rarefied_table.qza: The resulting rarefied feature table. + +| + +Description: +------------ +Subsample frequencies from all samples so that the sum of frequencies in each sample is equal to sampling-depth. + + +| + +</help> + <citations> + <citation type="doi">10.1186/s40168-017-0237-y</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>