Mercurial > repos > q2d2 > qiime2__quality_control__decontam_identify_batches
changeset 1:1c23691fa0c5 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit c7e80dcda727ce63b42aa8a946e9330310929797
| author | q2d2 |
|---|---|
| date | Mon, 03 Jun 2024 23:30:17 +0000 |
| parents | 2c425b0e5cdb |
| children | 31be63fff5db |
| files | qiime2__quality_control__decontam_identify_batches.xml |
| diffstat | 1 files changed, 12 insertions(+), 6 deletions(-) [+] |
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--- a/qiime2__quality_control__decontam_identify_batches.xml Thu Apr 25 21:18:00 2024 +0000 +++ b/qiime2__quality_control__decontam_identify_batches.xml Mon Jun 03 23:30:17 2024 +0000 @@ -6,14 +6,14 @@ --> <!-- This tool was automatically generated by: - q2galaxy (version: 2024.2.1) + q2galaxy (version: 2024.5.0) for: - qiime2 (version: 2024.2.0) + qiime2 (version: 2024.5.0) --> -<tool name="qiime2 quality-control decontam-identify-batches" id="qiime2__quality_control__decontam_identify_batches" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 quality-control decontam-identify-batches" id="qiime2__quality_control__decontam_identify_batches" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> <description>Identify contaminants in Batch Mode</description> <requirements> - <container type="docker">quay.io/qiime2/amplicon:2024.2</container> + <container type="docker">quay.io/qiime2/amplicon:2024.5</container> </requirements> <version_command>q2galaxy version quality_control</version_command> <command detect_errors="exit_code">q2galaxy run quality_control decontam_identify_batches '$inputs'</command> @@ -21,7 +21,7 @@ <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> - <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] ASV or OTU table which contaminate sequences will be identified from"> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] Feature table which contaminate sequences will be identified from"> <options options_filter_attribute="metadata.semantic_type"> <filter type="add_value" value="FeatureTable[Frequency]"/> </options> @@ -55,6 +55,12 @@ <validator type="expression" message="Please verify this parameter.">value != '__q2galaxy__::literal::None'</validator> </param> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="rep_seqs" type="data" format="qza" optional="true" label="rep_seqs: FeatureData[Sequence]" help="[optional] Representative Sequences table which contaminate seqeunces will be removed from"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[Sequence]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> + </param> <param name="filter_empty_features" type="select" label="filter_empty_features: Bool" help="[optional] If true, features which are not present in a split feature table are dropped." display="radio"> <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option> <option value="__q2galaxy__::literal::True">Yes</option> @@ -132,7 +138,7 @@ Outputs: -------- :batch_subset_tables.qza: Directory where feature tables split based on metadata and parameter split_column values should be written. -:decontam_scores.qza: The resulting table of scores from the decontam algorithm which scores each ASV or OTU on how likely they are to be a contaminant sequence +:decontam_scores.qza: The resulting table of scores from the decontam algorithm which scores each feature on how likely they are to be a contaminant sequence :score_histograms.qzv: The vizulaizer histograms for all decontam score objects generated from the pipeline |