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comparison qiime2__cutadapt__trim_paired.xml @ 6:aa7ffb412083 draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit b1fccfb38b4873cd4699743033449014a2978e7d
author q2d2
date Mon, 05 May 2025 18:41:54 +0000
parents e82bd0e0c7ad
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5:e82bd0e0c7ad 6:aa7ffb412083
1 <?xml version='1.0' encoding='utf-8'?> 1 <?xml version='1.0' encoding='utf-8'?>
2 <!-- 2 <!--
3 Copyright (c) 2024, QIIME 2 development team. 3 Copyright (c) 2025, 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: 2024.10.0) 9 q2galaxy (version: 2025.4.0)
10 for: 10 for:
11 qiime2 (version: 2024.10.1) 11 qiime2 (version: 2025.4.0)
12 --> 12 -->
13 <tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2025.4.0+q2galaxy.2025.4.0" profile="22.05" license="BSD-3-Clause">
14 <description>Find and remove adapters in demultiplexed paired-end sequences.</description> 14 <description>Find and remove adapters in demultiplexed paired-end sequences.</description>
15 <xrefs> 15 <xrefs>
16 <xref type="bio.tools">qiime2</xref> 16 <xref type="bio.tools">qiime2</xref>
17 </xrefs> 17 </xrefs>
18 <requirements> 18 <requirements>
19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container> 19 <container type="docker">quay.io/qiime2/amplicon:2025.4</container>
20 </requirements> 20 </requirements>
21 <version_command>q2galaxy version cutadapt</version_command> 21 <version_command>q2galaxy version cutadapt</version_command>
22 <command detect_errors="exit_code">q2galaxy run cutadapt trim_paired '$inputs'</command> 22 <command detect_errors="exit_code">q2galaxy run cutadapt trim_paired '$inputs'</command>
23 <configfiles> 23 <configfiles>
24 <inputs name="inputs" data_style="staging_path_and_source_path"/> 24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
77 <valid initial="string.printable"/> 77 <valid initial="string.printable"/>
78 </sanitizer> 78 </sanitizer>
79 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator> 79 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
80 </param> 80 </param>
81 </repeat> 81 </repeat>
82 <param name="forward_cut" type="integer" value="0" label="forward_cut: Int" help="[default: 0] Unconditionally remove bases from the beginning or end of each forward read. Cutting is applied before adapter trimming. Use a positive integer to remove bases from the 5' end and a negative integer to remove bases from the 3' end."/>
83 <param name="reverse_cut" type="integer" value="0" label="reverse_cut: Int" help="[default: 0] Unconditionally remove bases from the beginning or end of each reverse read. Cutting is applied before adapter trimming. Use a positive integer to remove bases from the 5' end and a negative integer to remove bases from the 3' end."/>
82 <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] Maximum allowed error rate."/> 84 <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] Maximum allowed error rate."/>
83 <param name="indels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="indels: Bool" help="[default: Yes] Allow insertions or deletions of bases when matching adapters."/> 85 <param name="indels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="indels: Bool" help="[default: Yes] Allow insertions or deletions of bases when matching adapters."/>
84 <param name="times" type="integer" min="1" value="1" label="times: Int % Range(1, None)" help="[default: 1] Remove multiple occurrences of an adapter if it is repeated, up to `times` times."/> 86 <param name="times" type="integer" min="1" value="1" label="times: Int % Range(1, None)" help="[default: 1] Remove multiple occurrences of an adapter if it is repeated, up to `times` times."/>
85 <param name="overlap" type="integer" min="1" value="3" label="overlap: Int % Range(1, None)" help="[default: 3] Require at least `overlap` bases of overlap between read and adapter for an adapter to be found."/> 87 <param name="overlap" type="integer" min="1" value="3" label="overlap: Int % Range(1, None)" help="[default: 3] Require at least `overlap` bases of overlap between read and adapter for an adapter to be found."/>
86 <param name="match_read_wildcards" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="match_read_wildcards: Bool" help="[default: No] Interpret IUPAC wildcards (e.g., N) in reads."/> 88 <param name="match_read_wildcards" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="match_read_wildcards: Bool" help="[default: No] Interpret IUPAC wildcards (e.g., N) in reads."/>