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comparison qiime2__dada2__denoise_ccs.xml @ 5:e73ff752eb45 draft default tip

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__dada2 commit 5f71b597c9495eae67a447744fded834f56ca1f7
author q2d2
date Wed, 30 Oct 2024 19:36:49 +0000
parents a22807aaff34
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4:a22807aaff34 5:e73ff752eb45
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: 2024.5.0) 9 q2galaxy (version: 2024.10.0)
10 for: 10 for:
11 qiime2 (version: 2024.5.0) 11 qiime2 (version: 2024.10.1)
12 --> 12 -->
13 <tool name="qiime2 dada2 denoise-ccs" id="qiime2__dada2__denoise_ccs" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause"> 13 <tool name="qiime2 dada2 denoise-ccs" id="qiime2__dada2__denoise_ccs" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
14 <description>Denoise and dereplicate single-end Pacbio CCS</description> 14 <description>Denoise and dereplicate single-end Pacbio CCS</description>
15 <xrefs>
16 <xref type="bio.tools">qiime2</xref>
17 </xrefs>
15 <requirements> 18 <requirements>
16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container> 19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
17 </requirements> 20 </requirements>
18 <version_command>q2galaxy version dada2</version_command> 21 <version_command>q2galaxy version dada2</version_command>
19 <command detect_errors="exit_code">q2galaxy run dada2 denoise_ccs '$inputs'</command> 22 <command detect_errors="exit_code">q2galaxy run dada2 denoise_ccs '$inputs'</command>
20 <configfiles> 23 <configfiles>
21 <inputs name="inputs" data_style="staging_path_and_source_path"/> 24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
31 <sanitizer> 34 <sanitizer>
32 <valid initial="string.printable"/> 35 <valid initial="string.printable"/>
33 </sanitizer> 36 </sanitizer>
34 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator> 37 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
35 </param> 38 </param>
36 <param name="adapter" type="text" label="adapter: Str" help="[required] Sequence of an adapter ligated to the 3' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded.">
37 <sanitizer>
38 <valid initial="string.printable"/>
39 </sanitizer>
40 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
41 </param>
42 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> 39 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
40 <conditional name="__q2galaxy__GUI__conditional__adapter__" label="adapter: Str">
41 <param name="__q2galaxy__GUI__select__" type="select" label="adapter: Str" help="[optional] Sequence of an adapter ligated to the 3' end. The adapter and any preceding bases are trimmed. Can contain IUPAC ambiguous nucleotide codes. Note, primer direction is 5' to 3'. Primers are removed before trim and filter step. Reads that do not contain the primer are discarded.">
42 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
43 <option value="__q2galaxy__::control::provide">Provide a value</option>
44 </param>
45 <when value="__q2galaxy__::control::default">
46 <param name="adapter" type="hidden" value="__q2galaxy__::literal::None"/>
47 </when>
48 <when value="__q2galaxy__::control::provide">
49 <param name="adapter" type="text">
50 <sanitizer>
51 <valid initial="string.printable"/>
52 </sanitizer>
53 </param>
54 </when>
55 </conditional>
43 <param name="max_mismatch" type="integer" value="2" label="max_mismatch: Int" help="[default: 2] The number of mismatches to tolerate when matching reads to primer sequences - see http://benjjneb.github.io/dada2/ for complete details."/> 56 <param name="max_mismatch" type="integer" value="2" label="max_mismatch: Int" help="[default: 2] The number of mismatches to tolerate when matching reads to primer sequences - see http://benjjneb.github.io/dada2/ for complete details."/>
44 <param name="indels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="indels: Bool" help="[default: No] Allow insertions or deletions of bases when matching adapters. Note that primer matching can be significantly slower, currently about 4x slower"/> 57 <param name="indels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="indels: Bool" help="[default: No] Allow insertions or deletions of bases when matching adapters. Note that primer matching can be significantly slower, currently about 4x slower"/>
45 <param name="trunc_len" type="integer" value="0" label="trunc_len: Int" help="[default: 0] Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed. Note: Since Pacbio CCS sequences were normally with very high quality scores, there is no need to truncate the Pacbio CCS sequences."/> 58 <param name="trunc_len" type="integer" value="0" label="trunc_len: Int" help="[default: 0] Position at which sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. If 0 is provided, no truncation or length filtering will be performed. Note: Since Pacbio CCS sequences were normally with very high quality scores, there is no need to truncate the Pacbio CCS sequences."/>
46 <param name="trim_left" type="integer" value="0" label="trim_left: Int" help="[default: 0] Position at which sequences should be trimmed due to low quality. This trims the 5' end of the of the input sequences, which will be the bases that were sequenced in the first cycles."/> 59 <param name="trim_left" type="integer" value="0" label="trim_left: Int" help="[default: 0] Position at which sequences should be trimmed due to low quality. This trims the 5' end of the of the input sequences, which will be the bases that were sequenced in the first cycles."/>
47 <param name="max_ee" type="float" value="2.0" label="max_ee: Float" help="[default: 2.0] Reads with number of expected errors higher than this value will be discarded."/> 60 <param name="max_ee" type="float" value="2.0" label="max_ee: Float" help="[default: 2.0] Reads with number of expected errors higher than this value will be discarded."/>