Mercurial > repos > q2d2 > qiime2__vsearch__fastq_stats
changeset 0:68c96beb62cf draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__vsearch commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 20:34:49 +0000 |
parents | |
children | 826f1e13fbd1 |
files | qiime2__vsearch__fastq_stats.xml test-data/.gitkeep |
diffstat | 1 files changed, 74 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__vsearch__fastq_stats.xml Mon Aug 29 20:34:49 2022 +0000 @@ -0,0 +1,74 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2022, 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: 2022.8.1) +for: + qiime2 (version: 2022.8.1) +--> +<tool name="qiime2 vsearch fastq-stats" id="qiime2__vsearch__fastq_stats" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Fastq stats with vsearch.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version vsearch</version_command> + <command detect_errors="aggressive">q2galaxy run vsearch fastq_stats '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="sequences" type="data" format="qza" label="sequences: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]" help="[required] Fastq sequences"> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> + <filter type="add_value" value="SampleData[SequencesWithQuality]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <conditional name="__q2galaxy__GUI__conditional__threads__"> + <param name="__q2galaxy__GUI__select__" type="select" label="threads: Int % Range(1, None) | Str % Choices('auto')" help="[default: 1] The number of threads used for computation."> + <option value="auto">auto (Str)</option> + <option value="__q2galaxy__::control::Int X Range(1__comma__ None)" selected="true">Provide a value (Int % Range(1, None))</option> + </param> + <when value="auto"> + <param name="threads" type="hidden" value="auto"/> + </when> + <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> + <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1] The number of threads used for computation."/> + </when> + </conditional> + </section> + </inputs> + <outputs> + <data name="visualization" format="qzv" label="${tool.name} on ${on_string}: visualization.qzv" from_work_dir="visualization.qzv"/> + </outputs> + <tests/> + <help> +QIIME 2: vsearch fastq-stats +============================ +Fastq stats with vsearch. + + +Outputs: +-------- +:visualization.qzv: <no description> + +| + +Description: +------------ +A fastq overview via vsearch's fastq_stats, fastq_eestats and fastq_eestats2 utilities. Please see https://github.com/torognes/vsearch for detailed documentation of these tools. + + +| + +</help> + <citations> + <citation type="doi">10.7717/peerj.2584</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>