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comparison qiime2__cutadapt__demux_single.xml @ 3:5551ccc407c9 draft

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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
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2:d8851a5b9360 3:5551ccc407c9
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2023, QIIME 2 development team. 3 Copyright (c) 2024, QIIME 2 development team.
4 4
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) 5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
6 --> 6 -->
7 <!-- 7 <!--
8 This tool was automatically generated by: 8 This tool was automatically generated by:
9 q2galaxy (version: 2023.5.0) 9 q2galaxy (version: 2024.2.1)
10 for: 10 for:
11 qiime2 (version: 2023.5.1) 11 qiime2 (version: 2024.2.0)
12 --> 12 -->
13 <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"> 13 <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">
14 <description>Demultiplex single-end sequence data with barcodes in-sequence.</description> 14 <description>Demultiplex single-end sequence data with barcodes in-sequence.</description>
15 <requirements> 15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2023.5</container> 16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
17 </requirements> 17 </requirements>
18 <version_command>q2galaxy version cutadapt</version_command> 18 <version_command>q2galaxy version cutadapt</version_command>
19 <command detect_errors="exit_code">q2galaxy run cutadapt demux_single '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run cutadapt demux_single '$inputs'</command>
20 <configfiles> 20 <configfiles>
21 <inputs name="inputs" data_style="paths"/> 21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
22 </configfiles> 22 </configfiles>
23 <inputs> 23 <inputs>
24 <param name="seqs" type="data" format="qza" label="seqs: MultiplexedSingleEndBarcodeInSequence" help="[required] The single-end sequences to be demultiplexed."> 24 <param name="seqs" type="data" format="qza" label="seqs: MultiplexedSingleEndBarcodeInSequence" help="[required] The single-end sequences to be demultiplexed.">
25 <options options_filter_attribute="metadata.semantic_type"> 25 <options options_filter_attribute="metadata.semantic_type">
26 <filter type="add_value" value="MultiplexedSingleEndBarcodeInSequence"/> 26 <filter type="add_value" value="MultiplexedSingleEndBarcodeInSequence"/>
44 <validator type="empty_field"/> 44 <validator type="empty_field"/>
45 </param> 45 </param>
46 </when> 46 </when>
47 </conditional> 47 </conditional>
48 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 48 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
49 <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."/>
50 <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."/>
49 <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%)."/> 51 <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%)."/>
50 <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 &quot;too many files&quot; errors related to sample quantity. Set to &quot;0&quot; to process all samples at once."/> 52 <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 &quot;too many files&quot; errors related to sample quantity. Set to &quot;0&quot; to process all samples at once."/>
51 <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."/> 53 <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."/>
52 <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1] Number of CPU cores to use."/>
53 </section> 54 </section>
54 </inputs> 55 </inputs>
55 <outputs> 56 <outputs>
56 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/> 57 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
57 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/> 58 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/>