Mercurial > repos > q2d2 > qiime2__feature_table__core_features
changeset 0:db935a4cfe8b 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 19:57:33 +0000 |
| parents | |
| children | 3ab02629e494 |
| files | qiime2__feature_table__core_features.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__core_features.xml Mon Aug 29 19:57:33 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 core-features" id="qiime2__feature_table__core_features" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Identify core features in 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 core_features '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] The feature table to use in core features calculations."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[Frequency]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="min_fraction" type="float" min="1e-06" max="0.999999" value="0.5" label="min_fraction: Float % Range(0.0, 1.0, inclusive_start=False)" help="[default: 0.5] The minimum fraction of samples that a feature must be observed in for that feature to be considered a core feature."/> + <param name="max_fraction" type="float" min="0.0" max="1.0" value="1.0" label="max_fraction: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 1.0] The maximum fraction of samples that a feature must be observed in for that feature to be considered a core feature."/> + <param name="steps" type="integer" min="2" value="11" label="steps: Int % Range(2, None)" help="[default: 11] The number of steps to take between `min_fraction` and `max_fraction` for core features calculations. This parameter has no effect if `min_fraction` and `max_fraction` are the same value."/> + </section> + </inputs> + <outputs> + <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> + </outputs> + <tests/> + <help> +QIIME 2: feature-table core-features +==================================== +Identify core features in table + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +Identify "core" features, which are features observed in a user-defined fraction of the samples. Since the core features are a function of the fraction of samples that the feature must be observed in to be considered core, this is computed over a range of fractions defined by the `min_fraction`, `max_fraction`, and `steps` parameters. + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>