Mercurial > repos > q2d2 > qiime2__quality_control__decontam_remove
changeset 0:2e8e3258af39 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 65e4952f33eb335528e8553150e9097e5ea8f556
| author | q2d2 |
|---|---|
| date | Thu, 08 Jun 2023 19:51:15 +0000 |
| parents | |
| children | 9edda646c9dd |
| files | qiime2__quality_control__decontam_remove.xml test-data/.gitkeep |
| diffstat | 1 files changed, 67 insertions(+), 0 deletions(-) [+] |
line wrap: on
line diff
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__quality_control__decontam_remove.xml Thu Jun 08 19:51:15 2023 +0000 @@ -0,0 +1,67 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2023, 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: 2023.5.0) +for: + qiime2 (version: 2023.5.1) +--> +<tool name="qiime2 quality-control decontam-remove" id="qiime2__quality_control__decontam_remove" version="2023.5.0+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> + <description>Removes contaminant</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2023.5</container> + </requirements> + <version_command>q2galaxy version quality_control</version_command> + <command detect_errors="exit_code">q2galaxy run quality_control decontam_remove '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="decontam_scores" type="data" format="qza" label="decontam_scores: FeatureData[DecontamScore]" help="[required] Output table from decontam identify"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureData[DecontamScore]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[DecontamScore]']</validator> + </param> + <param name="table" type="data" format="qza" label="table: FeatureTable[Frequency]" help="[required] ASV or OTU table which contaminate sequences will be identified from"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="FeatureTable[Frequency]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureTable[Frequency]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="threshold" type="float" value="0.1" label="threshold: Float" help="[default: 0.1] Select threshold cutoff for decontam algorithm scores"/> + </section> + </inputs> + <outputs> + <data name="filtered_table" format="qza" label="${tool.name} on ${on_string}: filtered_table.qza" from_work_dir="filtered_table.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: quality-control decontam-remove +======================================== +Removes contaminant + + +Outputs: +-------- +:filtered_table.qza: The resulting feature table of scores once contaminants are removed + +| + +Description: +------------ +This method removes contaminant sequences from an OTU or ASV table and returns the amended table to the user + + +| + +</help> + <citations> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>