| Previous changeset 5:0597a61cb4b5 (2024-10-30) |
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Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_table commit b1fccfb38b4873cd4699743033449014a2978e7d |
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modified:
qiime2__feature_table__filter_samples.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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| diff -r 0597a61cb4b5 -r 682d957756f9 qiime2__feature_table__filter_samples.xml --- a/qiime2__feature_table__filter_samples.xml Wed Oct 30 19:52:43 2024 +0000 +++ b/qiime2__feature_table__filter_samples.xml Mon May 05 18:51:54 2025 +0000 |
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| @@ -1,22 +1,22 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2024, QIIME 2 development team. +Copyright (c) 2025, 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: 2024.10.0) + q2galaxy (version: 2025.4.0) for: - qiime2 (version: 2024.10.1) + qiime2 (version: 2025.4.0) --> -<tool name="qiime2 feature-table filter-samples" id="qiime2__feature_table__filter_samples" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 feature-table filter-samples" id="qiime2__feature_table__filter_samples" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause"> <description>Filter samples from table</description> <xrefs> <xref type="bio.tools">qiime2</xref> </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2024.10</container> + <container type="docker">quay.io/qiime2/amplicon:2025.4</container> </requirements> <version_command>q2galaxy version feature_table</version_command> <command detect_errors="exit_code">q2galaxy run feature_table filter_samples '$inputs'</command> @@ -26,10 +26,10 @@ <inputs> <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency¹ | RelativeFrequency² | PresenceAbsence³ | Composition⁴]" help="[required] The feature table from which samples should be filtered."> <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> <filter type="add_value" value="FeatureTable[Frequency]"/> <filter type="add_value" value="FeatureTable[RelativeFrequency]"/> <filter type="add_value" value="FeatureTable[Composition]"/> - <filter type="add_value" value="FeatureTable[PresenceAbsence]"/> </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> @@ -85,7 +85,7 @@ <param name="source" value="filter_samples.test0.sample-metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> - <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__"/> + <param name="where" value="__ob__subject__cb__=__sq__subject-1__sq__"/> <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"> @@ -102,7 +102,7 @@ <param name="source" value="filter_samples.test1.sample-metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> - <param name="where" value="__ob__body-site__cb__ IN (__dq__left palm__dq____comma__ __dq__right palm__dq__)"/> + <param name="where" value="__ob__body-site__cb__ IN (__sq__left palm__sq____comma__ __sq__right palm__sq__)"/> <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"> @@ -119,7 +119,7 @@ <param name="source" value="filter_samples.test2.sample-metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> - <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__ AND __ob__body-site__cb__=__dq__gut__dq__"/> + <param name="where" value="__ob__subject__cb__=__sq__subject-1__sq__ AND __ob__body-site__cb__=__sq__gut__sq__"/> <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"> @@ -136,7 +136,7 @@ <param name="source" value="filter_samples.test3.sample-metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> - <param name="where" value="__ob__body-site__cb__=__dq__gut__dq__ OR __ob__reported-antibiotic-usage__cb__=__dq__Yes__dq__"/> + <param name="where" value="__ob__body-site__cb__=__sq__gut__sq__ OR __ob__reported-antibiotic-usage__cb__=__sq__Yes__sq__"/> <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"> @@ -153,7 +153,7 @@ <param name="source" value="filter_samples.test4.sample-metadata.tsv" ftype="qiime2.tabular"/> </conditional> </repeat> - <param name="where" value="__ob__subject__cb__=__dq__subject-1__dq__ AND NOT __ob__body-site__cb__=__dq__gut__dq__"/> + <param name="where" value="__ob__subject__cb__=__sq__subject-1__sq__ AND NOT __ob__body-site__cb__=__sq__gut__sq__"/> <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"> @@ -218,7 +218,7 @@ #. Set *"Metadata Source"* to ``sample-metadata.tsv`` - #. Set *"where"* to ``[subject]="subject-1"`` + #. Set *"where"* to ``[subject]='subject-1'`` #. Press the ``Execute`` button. @@ -237,7 +237,7 @@ #. Set *"Metadata Source"* to ``sample-metadata.tsv`` - #. Set *"where"* to ``[body-site] IN ("left palm", "right palm")`` + #. Set *"where"* to ``[body-site] IN ('left palm', 'right palm')`` #. Press the ``Execute`` button. @@ -256,7 +256,7 @@ #. Set *"Metadata Source"* to ``sample-metadata.tsv`` - #. Set *"where"* to ``[subject]="subject-1" AND [body-site]="gut"`` + #. Set *"where"* to ``[subject]='subject-1' AND [body-site]='gut'`` #. Press the ``Execute`` button. @@ -275,7 +275,7 @@ #. Set *"Metadata Source"* to ``sample-metadata.tsv`` - #. Set *"where"* to ``[body-site]="gut" OR [reported-antibiotic-usage]="Yes"`` + #. Set *"where"* to ``[body-site]='gut' OR [reported-antibiotic-usage]='Yes'`` #. Press the ``Execute`` button. @@ -294,7 +294,7 @@ #. Set *"Metadata Source"* to ``sample-metadata.tsv`` - #. Set *"where"* to ``[subject]="subject-1" AND NOT [body-site]="gut"`` + #. Set *"where"* to ``[subject]='subject-1' AND NOT [body-site]='gut'`` #. Press the ``Execute`` button. |
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