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comparison qiime2__cutadapt__demux_paired.xml @ 3:f21509fa9ed0 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 20:53:54 +0000
parents c6a8822e19f2
children 9b5a775806be
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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-paired" id="qiime2__cutadapt__demux_paired" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
14 <description>Demultiplex paired-end sequence data with barcodes in-sequence.</description> 14 <description>Demultiplex paired-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_paired '$inputs'</command> 19 <command detect_errors="exit_code">q2galaxy run cutadapt demux_paired '$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: MultiplexedPairedEndBarcodeInSequence" help="[required] The paired-end sequences to be demultiplexed."> 24 <param name="seqs" type="data" format="qza" label="seqs: MultiplexedPairedEndBarcodeInSequence" help="[required] The paired-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="MultiplexedPairedEndBarcodeInSequence"/> 26 <filter type="add_value" value="MultiplexedPairedEndBarcodeInSequence"/>
64 <param name="column" type="text" label="Column Name"> 64 <param name="column" type="text" label="Column Name">
65 <validator type="empty_field"/> 65 <validator type="empty_field"/>
66 </param> 66 </param>
67 </when> 67 </when>
68 </conditional> 68 </conditional>
69 <param name="forward_cut" type="integer" value="0" label="forward_cut: Int" help="[default: 0] Remove the specified number of bases from the forward 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. If --p-mixed-orientation is set, then both --p-forward-cut and --p-reverse-cut must be set to the same value."/>
70 <param name="reverse_cut" type="integer" value="0" label="reverse_cut: Int" help="[default: 0] Remove the specified number of bases from the reverse 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. If --p-mixed-orientation is set, then both --p-forward-cut and --p-reverse-cut must be set to the same value."/>
71 <param name="anchor_forward_barcode" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="anchor_forward_barcode: Bool" help="[default: No] Anchor the forward barcode. The barcode is then expected to occur in full length at the beginning (5' end) of the forward sequence. Can speed up demultiplexing if used."/>
72 <param name="anchor_reverse_barcode" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="anchor_reverse_barcode: Bool" help="[default: No] Anchor the reverse barcode. The barcode is then expected to occur in full length at the beginning (5' end) of the reverse sequence. Can speed up demultiplexing if used."/>
69 <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."/> 73 <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."/>
70 <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."/> 74 <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."/>
71 <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."/> 75 <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."/>
72 <param name="mixed_orientation" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="mixed_orientation: Bool" help="[default: No] Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file)."/> 76 <param name="mixed_orientation" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="mixed_orientation: Bool" help="[default: No] Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file)."/>
73 <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1] Number of CPU cores to use."/>
74 </section> 77 </section>
75 </inputs> 78 </inputs>
76 <outputs> 79 <outputs>
77 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/> 80 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
78 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/> 81 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/>