| Previous changeset 2:78538c1b0993 (2023-06-08) Next changeset 4:6c8f74d8df6d (2024-06-03) |
|
Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 389df0134cd0763dcf02aac6e623fc15f8861c1e |
|
modified:
qiime2__feature_table__filter_features_conditionally.xml test-data/filter_features.test0.feature-table.qza test-data/filter_features_conditionally.test0.feature-table.qza test-data/filter_samples.test0.feature-table.qza test-data/filter_samples.test1.feature-table.qza test-data/filter_samples.test2.feature-table.qza test-data/filter_samples.test3.feature-table.qza test-data/filter_samples.test4.feature-table.qza test-data/filter_samples.test5.feature-table.qza test-data/filter_samples.test6.feature-table.qza test-data/group.test0.feature-table.qza 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 test-data/merge_seqs.test0.seqs1.qza test-data/merge_seqs.test0.seqs2.qza test-data/merge_taxa.test0.tax1.qza test-data/merge_taxa.test0.tax2.qza test-data/summarize.test0.feature-table.qza test-data/tabulate_seqs.test0.rep-seqs.qza |
|
added:
test-data/summarize_plus.test0.feature-table.qza test-data/tabulate_feature_frequencies.test0.feature-table.qza test-data/tabulate_sample_frequencies.test0.feature-table.qza test-data/tabulate_seqs.test1.rep-seqs-single-taxon.qza test-data/tabulate_seqs.test1.single-taxonomy.qza test-data/tabulate_seqs.test2.multi-taxonomy/.order test-data/tabulate_seqs.test2.multi-taxonomy/GG1.qza test-data/tabulate_seqs.test2.multi-taxonomy/GG2.qza test-data/tabulate_seqs.test2.rep-seqs-multi-taxon.qza |
| b |
| diff -r 78538c1b0993 -r 09226feca49a qiime2__feature_table__filter_features_conditionally.xml --- a/qiime2__feature_table__filter_features_conditionally.xml Thu Jun 08 19:47:43 2023 +0000 +++ b/qiime2__feature_table__filter_features_conditionally.xml Thu Apr 25 21:14:40 2024 +0000 |
| [ |
| @@ -1,37 +1,40 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2023, QIIME 2 development team. +Copyright (c) 2024, 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: 2023.5.0) + q2galaxy (version: 2024.2.1) for: - qiime2 (version: 2023.5.1) + qiime2 (version: 2024.2.0) --> -<tool name="qiime2 feature-table filter-features-conditionally" id="qiime2__feature_table__filter_features_conditionally" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 feature-table filter-features-conditionally" id="qiime2__feature_table__filter_features_conditionally" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>Filter features from a table based on abundance and prevalence</description> <requirements> - <container type="docker">quay.io/qiime2/core:2023.5</container> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> </requirements> <version_command>q2galaxy version feature_table</version_command> <command detect_errors="exit_code">q2galaxy run feature_table filter_features_conditionally '$inputs'</command> <configfiles> - <inputs name="inputs" data_style="paths"/> + <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The feature table from which features should be filtered."> <options options_filter_attribute="metadata.semantic_type"> - <filter type="add_value" value="FeatureTable[Frequency]"/> <filter type="add_value" value="FeatureTable[Composition]"/> <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> + <filter type="add_value" value="FeatureTable[Frequency]"/> <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Composition]', 'FeatureTable[Frequency]', 'FeatureTable[PresenceAbsence]', 'FeatureTable[RelativeFrequency]']</validator> </param> <param name="abundance" type="float" min="0" max="0.999999" value="" label="abundance: Float % Range(0, 1)" help="[required] The minimum relative abundance for a feature to be retained."/> <param name="prevalence" type="float" min="0" max="0.999999" value="" label="prevalence: Float % Range(0, 1)" help="[required] The minimum portion of samples that a feature must have a relative abundance of at least `abundance` to be retained."/> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="allow_empty_table" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="allow_empty_table: Bool" help="[default: No] If true, the filtered table may be empty. Default behavior is to raise an error if the filtered table is empty."/> + </section> </inputs> <outputs> <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/filter_features.test0.feature-table.qza |
| b |
| Binary file test-data/filter_features.test0.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/filter_features_conditionally.test0.feature-table.qza |
| b |
| Binary file test-data/filter_features_conditionally.test0.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/filter_samples.test0.feature-table.qza |
| b |
| Binary file test-data/filter_samples.test0.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/filter_samples.test1.feature-table.qza |
| b |
| Binary file test-data/filter_samples.test1.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/filter_samples.test2.feature-table.qza |
| b |
| Binary file test-data/filter_samples.test2.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/filter_samples.test3.feature-table.qza |
| b |
| Binary file test-data/filter_samples.test3.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/filter_samples.test4.feature-table.qza |
| b |
| Binary file test-data/filter_samples.test4.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/filter_samples.test5.feature-table.qza |
| b |
| Binary file test-data/filter_samples.test5.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/filter_samples.test6.feature-table.qza |
| b |
| Binary file test-data/filter_samples.test6.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/group.test0.feature-table.qza |
| b |
| Binary file test-data/group.test0.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/merge.test0.feature-table1.qza |
| b |
| Binary file test-data/merge.test0.feature-table1.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/merge.test0.feature-table2.qza |
| b |
| Binary file test-data/merge.test0.feature-table2.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/merge.test1.feature-table1.qza |
| b |
| Binary file test-data/merge.test1.feature-table1.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/merge.test1.feature-table2.qza |
| b |
| Binary file test-data/merge.test1.feature-table2.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/merge.test1.feature-table3.qza |
| b |
| Binary file test-data/merge.test1.feature-table3.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/merge_seqs.test0.seqs1.qza |
| b |
| Binary file test-data/merge_seqs.test0.seqs1.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/merge_seqs.test0.seqs2.qza |
| b |
| Binary file test-data/merge_seqs.test0.seqs2.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/merge_taxa.test0.tax1.qza |
| b |
| Binary file test-data/merge_taxa.test0.tax1.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/merge_taxa.test0.tax2.qza |
| b |
| Binary file test-data/merge_taxa.test0.tax2.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/summarize.test0.feature-table.qza |
| b |
| Binary file test-data/summarize.test0.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/summarize_plus.test0.feature-table.qza |
| b |
| Binary file test-data/summarize_plus.test0.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/tabulate_feature_frequencies.test0.feature-table.qza |
| b |
| Binary file test-data/tabulate_feature_frequencies.test0.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/tabulate_sample_frequencies.test0.feature-table.qza |
| b |
| Binary file test-data/tabulate_sample_frequencies.test0.feature-table.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/tabulate_seqs.test0.rep-seqs.qza |
| b |
| Binary file test-data/tabulate_seqs.test0.rep-seqs.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/tabulate_seqs.test1.rep-seqs-single-taxon.qza |
| b |
| Binary file test-data/tabulate_seqs.test1.rep-seqs-single-taxon.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/tabulate_seqs.test1.single-taxonomy.qza |
| b |
| Binary file test-data/tabulate_seqs.test1.single-taxonomy.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/tabulate_seqs.test2.multi-taxonomy/.order --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/tabulate_seqs.test2.multi-taxonomy/.order Thu Apr 25 21:14:40 2024 +0000 |
| b |
| @@ -0,0 +1,2 @@ +GG1 +GG2 |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/tabulate_seqs.test2.multi-taxonomy/GG1.qza |
| b |
| Binary file test-data/tabulate_seqs.test2.multi-taxonomy/GG1.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/tabulate_seqs.test2.multi-taxonomy/GG2.qza |
| b |
| Binary file test-data/tabulate_seqs.test2.multi-taxonomy/GG2.qza has changed |
| b |
| diff -r 78538c1b0993 -r 09226feca49a test-data/tabulate_seqs.test2.rep-seqs-multi-taxon.qza |
| b |
| Binary file test-data/tabulate_seqs.test2.rep-seqs-multi-taxon.qza has changed |