| Previous changeset 6:4190dbce3775 (2025-05-05) Next changeset 8:5545c2f27907 (2025-11-01) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit 9436cc47c72b58a6a3d3a5c2ee075689c2926ef0 |
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modified:
qiime2__feature_table__filter_features.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/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.test0.rep-seqs.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/GG1.qza test-data/tabulate_seqs.test2.multi-taxonomy/GG2.qza test-data/tabulate_seqs.test2.rep-seqs-multi-taxon.qza |
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added:
test-data/filter_features.test1.feature-table.qza test-data/filter_features.test1.sequences.qza |
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| diff -r 4190dbce3775 -r a4ee4441998f qiime2__feature_table__filter_features.xml --- a/qiime2__feature_table__filter_features.xml Mon May 05 18:52:08 2025 +0000 +++ b/qiime2__feature_table__filter_features.xml Tue Jul 15 22:00:10 2025 +0000 |
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| @@ -6,17 +6,17 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2025.4.0) + q2galaxy (version: 2025.7.0) for: - qiime2 (version: 2025.4.0) + qiime2 (version: 2025.7.0) --> -<tool name="qiime2 feature-table filter-features" id="qiime2__feature_table__filter_features" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 feature-table filter-features" id="qiime2__feature_table__filter_features" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause"> <description>Filter features from table</description> <xrefs> <xref type="bio.tools">qiime2</xref> </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2025.4</container> + <container type="docker">quay.io/qiime2/amplicon:2025.7</container> </requirements> <version_command>q2galaxy version feature_table</version_command> <command detect_errors="exit_code">q2galaxy run feature_table filter_features '$inputs'</command> @@ -85,6 +85,22 @@ </assert_contents> </output> </test> + <test> + <param name="table" value="filter_features.test1.feature-table.qza" ftype="qza"/> + <repeat name="metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" value="qza"/> + <param name="source" value="filter_features.test1.sequences.qza" ftype="qza"/> + </conditional> + </repeat> + <output name="filtered_table" ftype="qza"> + <assert_contents> + <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> + <has_line_matching expression="type: FeatureTable\[Frequency\]"/> + </has_archive_member> + </assert_contents> + </output> + </test> </tests> <help> QIIME 2: feature-table filter-features @@ -100,7 +116,7 @@ Description: ------------ -Filter features from table based on frequency and/or metadata. Any samples with a frequency of zero after feature filtering will also be removed. See the filtering tutorial on https://docs.qiime2.org for additional details. +Filter features from table based on frequency and/or metadata. Any samples with a frequency of zero after feature filtering will also be removed. Examples: --------- @@ -116,6 +132,25 @@ #. Press the ``Execute`` button. +filter_features_sequences +************************* +| Retain only features that are represented in the collection of sequences provided as metadata. This is useful, for example, for removing sequences that are identified as chimeric. To learn about using Artifacts as Metadata, as is performed here, see https://use.qiime2.org/en/latest/how-to-guides/artifacts-as-metadata.html +Using the ``qiime2 feature-table filter-features`` tool: + #. Set *"table"* to ``#: feature-table.qza`` + #. Expand the ``additional options`` section + + - For *"metadata"*: + + - Press the ``+ Insert metadata`` button to set up the next steps. + + #. Change to ``Metadata from Artifact`` + #. Set *"Metadata Source"* to ``sequences.qza`` + + + + #. Press the ``Execute`` button. + + | |
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