Mercurial > repos > q2d2 > qiime2__quality_filter__q_score
comparison qiime2__quality_filter__q_score.xml @ 0:8bf2383917c3 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 20:22:53 +0000 |
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children | 2c4de53c8903 |
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1 <?xml version='1.0' encoding='utf-8'?> | |
2 <!-- | |
3 Copyright (c) 2022, QIIME 2 development team. | |
4 | |
5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) | |
6 --> | |
7 <!-- | |
8 This tool was automatically generated by: | |
9 q2galaxy (version: 2022.8.1) | |
10 for: | |
11 qiime2 (version: 2022.8.1) | |
12 --> | |
13 <tool name="qiime2 quality-filter q-score" id="qiime2__quality_filter__q_score" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
14 <description>Quality filter based on sequence quality scores.</description> | |
15 <requirements> | |
16 <container type="docker">quay.io/qiime2/core:2022.8</container> | |
17 </requirements> | |
18 <version_command>q2galaxy version quality_filter</version_command> | |
19 <command detect_errors="aggressive">q2galaxy run quality_filter q_score '$inputs'</command> | |
20 <configfiles> | |
21 <inputs name="inputs" data_style="paths"/> | |
22 </configfiles> | |
23 <inputs> | |
24 <param name="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²" help="[required] The demultiplexed sequence data to be quality filtered."> | |
25 <options options_filter_attribute="metadata.semantic_type"> | |
26 <filter type="add_value" value="SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]"/> | |
27 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/> | |
28 </options> | |
29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]']</validator> | |
30 </param> | |
31 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
32 <param name="min_quality" type="integer" value="4" label="min_quality: Int" help="[default: 4] The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores."/> | |
33 <param name="quality_window" type="integer" value="3" label="quality_window: Int" help="[default: 3] The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read."/> | |
34 <param name="min_length_fraction" type="float" value="0.75" label="min_length_fraction: Float" help="[default: 0.75] The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length."/> | |
35 <param name="max_ambiguous" type="integer" value="0" label="max_ambiguous: Int" help="[default: 0] The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min_length_fraction`."/> | |
36 </section> | |
37 </inputs> | |
38 <outputs> | |
39 <data name="filtered_sequences" format="qza" label="${tool.name} on ${on_string}: filtered_sequences.qza" from_work_dir="filtered_sequences.qza"/> | |
40 <data name="filter_stats" format="qza" label="${tool.name} on ${on_string}: filter_stats.qza" from_work_dir="filter_stats.qza"/> | |
41 </outputs> | |
42 <tests/> | |
43 <help> | |
44 QIIME 2: quality-filter q-score | |
45 =============================== | |
46 Quality filter based on sequence quality scores. | |
47 | |
48 | |
49 Outputs: | |
50 -------- | |
51 :filtered_sequences.qza: The resulting quality-filtered sequences. | |
52 :filter_stats.qza: Summary statistics of the filtering process. | |
53 | |
54 | | |
55 | |
56 Description: | |
57 ------------ | |
58 This method filters sequence based on quality scores and the presence of ambiguous base calls. | |
59 | |
60 | |
61 | | |
62 | |
63 </help> | |
64 <citations> | |
65 <citation type="doi">10.1038/nmeth.2276</citation> | |
66 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
67 </citations> | |
68 </tool> |