Mercurial > repos > q2d2 > qiime2__cutadapt__demux_single
changeset 3:5551ccc407c9 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author | q2d2 |
---|---|
date | Thu, 25 Apr 2024 20:53:30 +0000 |
parents | d8851a5b9360 |
children | fcb0c9bd84a3 |
files | qiime2__cutadapt__demux_single.xml test-data/demux_paired.test0.seqs.qza test-data/demux_single.test0.seqs.qza |
diffstat | 3 files changed, 8 insertions(+), 7 deletions(-) [+] |
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--- a/qiime2__cutadapt__demux_single.xml Thu Jun 08 19:34:49 2023 +0000 +++ b/qiime2__cutadapt__demux_single.xml Thu Apr 25 20:53:30 2024 +0000 @@ -1,24 +1,24 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2023, QIIME 2 development team. +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: 2023.5.0) + q2galaxy (version: 2024.2.1) for: - qiime2 (version: 2023.5.1) + qiime2 (version: 2024.2.0) --> -<tool name="qiime2 cutadapt demux-single" id="qiime2__cutadapt__demux_single" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> +<tool name="qiime2 cutadapt demux-single" id="qiime2__cutadapt__demux_single" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> <description>Demultiplex single-end sequence data with barcodes in-sequence.</description> <requirements> - <container type="docker">quay.io/qiime2/core:2023.5</container> + <container type="docker">quay.io/qiime2/amplicon:2024.2</container> </requirements> <version_command>q2galaxy version cutadapt</version_command> <command detect_errors="exit_code">q2galaxy run cutadapt demux_single '$inputs'</command> <configfiles> - <inputs name="inputs" data_style="paths"/> + <inputs name="inputs" data_style="staging_path_and_source_path"/> </configfiles> <inputs> <param name="seqs" type="data" format="qza" label="seqs: MultiplexedSingleEndBarcodeInSequence" help="[required] The single-end sequences to be demultiplexed."> @@ -46,10 +46,11 @@ </when> </conditional> <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="cut" type="integer" value="0" label="cut: Int" help="[default: 0] Remove the specified number of bases from the sequences. Bases are removed before demultiplexing. If a positive value is provided, bases are removed from the beginning of the sequences. If a negative value is provided, bases are removed from the end of the sequences."/> + <param name="anchor_barcode" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="anchor_barcode: Bool" help="[default: No] Anchor the barcode. The barcode is then expected to occur in full length at the beginning (5' end) of the sequence. Can speed up demultiplexing if used."/> <param name="error_rate" type="float" min="0" max="1" value="0.1" label="error_rate: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.1] The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%)."/> <param name="batch_size" type="integer" min="0" value="0" label="batch_size: Int % Range(0, None)" help="[default: 0] The number of samples cutadapt demultiplexes concurrently. Demultiplexing in smaller batches will yield the same result with marginal speed loss, and may solve "too many files" errors related to sample quantity. Set to "0" to process all samples at once."/> <param name="minimum_length" type="integer" min="1" value="1" label="minimum_length: Int % Range(1, None)" help="[default: 1] Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records."/> - <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1] Number of CPU cores to use."/> </section> </inputs> <outputs>