Mercurial > repos > q2d2 > qiime2__quality_control__decontam_identify_batches
changeset 0:2c425b0e5cdb draft default tip
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
| author | q2d2 |
|---|---|
| date | Thu, 25 Apr 2024 21:18:00 +0000 |
| parents | |
| children | |
| files | qiime2__quality_control__decontam_identify_batches.xml test-data/.gitkeep |
| diffstat | 1 files changed, 151 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__quality_control__decontam_identify_batches.xml Thu Apr 25 21:18:00 2024 +0000 @@ -0,0 +1,151 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2024, 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: 2024.2.1) +for: + qiime2 (version: 2024.2.0) +--> +<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"> + <description>Identify contaminants in Batch Mode</description> + <requirements> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> + </requirements> + <version_command>q2galaxy version quality_control</version_command> + <command detect_errors="exit_code">q2galaxy run quality_control decontam_identify_batches '$inputs'</command> + <configfiles> + <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"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[Frequency]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> + </param> + <repeat name="metadata" min="1" help="[required] metadata file indicating which samples in the experiment are control samples, assumes sample names in file correspond to the `table` input parameter" 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> + <param name="split_column" type="text" label="split_column: Str" help="[required] input metadata columns that you wish to subset the ASV table byNote: Column names must be in quotes and delimited by a space"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + <param name="method" type="select" label="method: Str % Choices('combined', 'frequency', 'prevalence')" display="radio"> + <option value="__q2galaxy__::literal::None">Selection required</option> + <option value="combined">combined</option> + <option value="frequency">frequency</option> + <option value="prevalence">prevalence</option> + <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="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> + <option value="__q2galaxy__::literal::False">No</option> + </param> + <conditional name="__q2galaxy__GUI__conditional__freq_concentration_column__" label="freq_concentration_column: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="freq_concentration_column: Str" help="[optional] Input column name that has concentration information for the samples"> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="freq_concentration_column" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="freq_concentration_column" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <conditional name="__q2galaxy__GUI__conditional__prev_control_column__" label="prev_control_column: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="prev_control_column: Str" help="[optional] Input column name containing experimental or control sample metadata"> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="prev_control_column" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="prev_control_column" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <conditional name="__q2galaxy__GUI__conditional__prev_control_indicator__" label="prev_control_indicator: Str"> + <param name="__q2galaxy__GUI__select__" type="select" label="prev_control_indicator: Str" help="[optional] indicate the control sample identifier (e.g. "control" or "blank")"> + <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option> + <option value="__q2galaxy__::control::provide">Provide a value</option> + </param> + <when value="__q2galaxy__::control::default"> + <param name="prev_control_indicator" type="hidden" value="__q2galaxy__::literal::None"/> + </when> + <when value="__q2galaxy__::control::provide"> + <param name="prev_control_indicator" type="text"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + </param> + </when> + </conditional> + <param name="threshold" type="float" value="0.1" label="threshold: Float" help="[default: 0.1] Select threshold cutoff for decontam algorithm scores"/> + <param name="weighted" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="weighted: Bool" help="[default: Yes] weight the decontam scores by their associated read number"/> + <param name="bin_size" type="float" value="0.02" label="bin_size: Float" help="[default: 0.02] Select bin size for the histogram"/> + </section> + </inputs> + <outputs> + <collection name="batch_subset_tables" type="list"> + <discover_datasets directory="batch_subset_tables" pattern="__name_and_ext__"/> + </collection> + <collection name="decontam_scores" type="list"> + <discover_datasets directory="decontam_scores" pattern="__name_and_ext__"/> + </collection> + <data name="score_histograms" format="qzv" label="${tool.name} on ${on_string}: score_histograms.qzv" from_work_dir="score_histograms.qzv"/> + </outputs> + <tests/> + <help> +QIIME 2: quality-control decontam-identify-batches +================================================== +Identify contaminants in Batch Mode + + +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 +:score_histograms.qzv: The vizulaizer histograms for all decontam score objects generated from the pipeline + +| + +Description: +------------ +This method breaks an ASV table into batches based on the given metadata and identifies contaminant sequences from an OTU or ASV table and reports them to the user + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>