Mercurial > repos > q2d2 > qiime2__vsearch__cluster_features_de_novo
changeset 5:31b630d08cda draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 5f71b597c9495eae67a447744fded834f56ca1f7
| author | q2d2 |
|---|---|
| date | Wed, 30 Oct 2024 19:59:48 +0000 |
| parents | 3377d6ce369c |
| children | |
| files | qiime2__vsearch__cluster_features_de_novo.xml test-data/.gitkeep test-data/cluster_features_de_novo.test0.seqs1.qza test-data/cluster_features_de_novo.test0.table1.qza |
| diffstat | 3 files changed, 45 insertions(+), 5 deletions(-) [+] |
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--- a/qiime2__vsearch__cluster_features_de_novo.xml Mon Jun 03 23:32:27 2024 +0000 +++ b/qiime2__vsearch__cluster_features_de_novo.xml Wed Oct 30 19:59:48 2024 +0000 @@ -6,14 +6,17 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2024.5.0) + q2galaxy (version: 2024.10.0) for: - qiime2 (version: 2024.5.0) + qiime2 (version: 2024.10.1) --> -<tool name="qiime2 vsearch cluster-features-de-novo" id="qiime2__vsearch__cluster_features_de_novo" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 vsearch cluster-features-de-novo" id="qiime2__vsearch__cluster_features_de_novo" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> <description>De novo clustering of features.</description> + <xrefs> + <xref type="bio.tools">qiime2</xref> + </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2024.5</container> + <container type="docker">quay.io/qiime2/amplicon:2024.10</container> </requirements> <version_command>q2galaxy version vsearch</version_command> <command detect_errors="exit_code">q2galaxy run vsearch cluster_features_de_novo '$inputs'</command> @@ -45,7 +48,28 @@ <data name="clustered_table" format="qza" label="${tool.name} on ${on_string}: clustered_table.qza" from_work_dir="clustered_table.qza"/> <data name="clustered_sequences" format="qza" label="${tool.name} on ${on_string}: clustered_sequences.qza" from_work_dir="clustered_sequences.qza"/> </outputs> - <tests/> + <tests> + <test> + <param name="sequences" value="cluster_features_de_novo.test0.seqs1.qza" ftype="qza"/> + <param name="table" value="cluster_features_de_novo.test0.table1.qza" ftype="qza"/> + <param name="perc_identity" value="0.97"/> + <param name="strand" value="plus"/> + <output name="clustered_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> + <output name="clustered_sequences" 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: FeatureData\[Sequence\]"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: vsearch cluster-features-de-novo ========================================= @@ -63,6 +87,22 @@ ------------ Given a feature table and the associated feature sequences, cluster the features based on user-specified percent identity threshold of their sequences. This is not a general-purpose de novo clustering method, but rather is intended to be used for clustering the results of quality-filtering/dereplication methods, such as DADA2, or for re-clustering a FeatureTable at a lower percent identity than it was originally clustered at. When a group of features in the input table are clustered into a single feature, the frequency of that single feature in a given sample is the sum of the frequencies of the features that were clustered in that sample. Feature identifiers and sequences will be inherited from the centroid feature of each cluster. See the vsearch documentation for details on how sequence clustering is performed. +Examples: +--------- + +cluster_features_de_novo +************************ +Using the ``qiime2 vsearch cluster-features-de-novo`` tool: + #. Set *"sequences"* to ``#: seqs1.qza`` + #. Set *"table"* to ``#: table1.qza`` + #. Set *"perc_identity"* to ``0.97`` + #. Expand the ``additional options`` section + + - Leave *"strand"* as its default value of ``plus`` + + #. Press the ``Execute`` button. + + |