Mercurial > repos > q2d2 > qiime2__demux__filter_samples
changeset 8:4c13a2d68a2a draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__demux commit 64ed09f1f1c680ad8373d261bd6be43a4f8a8d5b
| author | q2d2 |
|---|---|
| date | Sat, 01 Nov 2025 17:11:09 +0000 |
| parents | e3d4217c9a64 |
| children | |
| files | qiime2__demux__filter_samples.xml test-data/emp_single.test0.sequences.qza test-data/summarize.test0.demux.qza |
| diffstat | 3 files changed, 21 insertions(+), 20 deletions(-) [+] |
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--- a/qiime2__demux__filter_samples.xml Tue Jul 15 21:49:18 2025 +0000 +++ b/qiime2__demux__filter_samples.xml Sat Nov 01 17:11:09 2025 +0000 @@ -6,17 +6,17 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2025.7.0) + q2galaxy (version: 2025.10.0) for: - qiime2 (version: 2025.7.0) + qiime2 (version: 2025.10.0) --> -<tool name="qiime2 demux filter-samples" id="qiime2__demux__filter_samples" version="2025.7.0+q2galaxy.2025.7.0" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 demux filter-samples" id="qiime2__demux__filter_samples" version="2025.10.0+q2galaxy.2025.10.0" profile="22.05" license="BSD-3-Clause"> <description>Filter samples out of demultiplexed data.</description> <xrefs> <xref type="bio.tools">qiime2</xref> </xrefs> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2025.7</container> + <container type="docker">quay.io/qiime2/amplicon:2025.10</container> </requirements> <version_command>q2galaxy version demux</version_command> <command detect_errors="exit_code">q2galaxy run demux filter_samples '$inputs'</command> @@ -26,27 +26,27 @@ <inputs> <param name="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality¹ | PairedEndSequencesWithQuality² | JoinedSequencesWithQuality³]" help="[required] The demultiplexed data from which samples should be filtered."> <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="SampleData[SequencesWithQuality]"/> <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/> - <filter type="add_value" value="SampleData[SequencesWithQuality]"/> </options> <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator> </param> - <repeat name="metadata" min="1" help="[required] Sample metadata indicating which sample ids to filter. The optional `where` parameter may be used to filter ids based on specified conditions in the metadata. The optional `exclude_ids` parameter may be used to exclude the ids specified in the metadata from the filter." title="metadata: Metadata"> - <conditional name="__q2galaxy__GUI__conditional__metadata__"> - <param name="type" type="select" label="metadata: Metadata"> - <option value="tsv" selected="true">Metadata from TSV</option> - <option value="qza">Metadata from Artifact</option> - </param> - <when value="tsv"> - <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> - </when> - <when value="qza"> - <param name="source" type="data" format="qza" label="Metadata Source"/> - </when> - </conditional> - </repeat> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <repeat name="metadata" help="[optional] Sample metadata indicating which sample ids to filter. The optional `where` parameter may be used to filter ids based on specified conditions in the metadata. The optional `exclude_ids` parameter may be used to exclude the ids specified in the metadata from the filter." title="metadata: Metadata"> + <conditional name="__q2galaxy__GUI__conditional__metadata__"> + <param name="type" type="select" label="metadata: Metadata"> + <option value="tsv" selected="true">Metadata from TSV</option> + <option value="qza">Metadata from Artifact</option> + </param> + <when value="tsv"> + <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/> + </when> + <when value="qza"> + <param name="source" type="data" format="qza" label="Metadata Source"/> + </when> + </conditional> + </repeat> <conditional name="__q2galaxy__GUI__conditional__where__" label="where: Str"> <param name="__q2galaxy__GUI__select__" type="select" label="where: Str" help="[optional] Optional SQLite WHERE clause specifying sample metadata criteria that must be met to be included in the filtered data. If not provided, all samples in `metadata` that are also in the demultiplexed data will be retained."> <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> @@ -64,6 +64,7 @@ </when> </conditional> <param name="exclude_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="exclude_ids: Bool" help="[default: No] Defaults to False. If True, the samples selected by the `metadata` and optional `where` parameter will be excluded from the filtered data."/> + <param name="remove_empty" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="remove_empty: Bool" help="[default: No] Remove samples with empty FASTQ files."/> </section> </inputs> <outputs> @@ -84,7 +85,7 @@ Description: ------------ -Filter samples indicated in given metadata out of demultiplexed data. Specific samples can be further selected with the WHERE clause, and the `exclude_ids` parameter allows for filtering of all samples not specified. +Filter samples indicated in given metadata out of demultiplexed data or filter out empty samples. Specific samples can be further selected with the WHERE clause, and the `exclude_ids` parameter allows for filtering of all samples not specified. |