Mercurial > repos > q2d2 > qiime2__feature_classifier__extract_reads
comparison qiime2__feature_classifier__extract_reads.xml @ 0:f7557e88befd draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__feature_classifier commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 19:50:33 +0000 |
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children | 920dbc6886d7 |
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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 feature-classifier extract-reads" id="qiime2__feature_classifier__extract_reads" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
14 <description>Extract reads from reference sequences.</description> | |
15 <requirements> | |
16 <container type="docker">quay.io/qiime2/core:2022.8</container> | |
17 </requirements> | |
18 <version_command>q2galaxy version feature_classifier</version_command> | |
19 <command detect_errors="aggressive">q2galaxy run feature_classifier extract_reads '$inputs'</command> | |
20 <configfiles> | |
21 <inputs name="inputs" data_style="paths"/> | |
22 </configfiles> | |
23 <inputs> | |
24 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]"> | |
25 <options options_filter_attribute="metadata.semantic_type"> | |
26 <filter type="add_value" value="FeatureData[Sequence]"/> | |
27 </options> | |
28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator> | |
29 </param> | |
30 <param name="f_primer" type="text" label="f_primer: Str" help="[required] forward primer sequence (5' -> 3')."> | |
31 <sanitizer> | |
32 <valid initial="string.printable"/> | |
33 </sanitizer> | |
34 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> | |
35 </param> | |
36 <param name="r_primer" type="text" label="r_primer: Str" help="[required] reverse primer sequence (5' -> 3'). Do not use reverse-complemented primer sequence."> | |
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) > 0</validator> | |
41 </param> | |
42 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
43 <param name="trim_right" type="integer" value="0" label="trim_right: Int" help="[default: 0] trim_right nucleotides are removed from the 3' end if trim_right is positive. Applied before trunc_len and trim_left."/> | |
44 <param name="trunc_len" type="integer" value="0" label="trunc_len: Int" help="[default: 0] read is cut to trunc_len if trunc_len is positive. Applied after trim_right but before trim_left."/> | |
45 <param name="trim_left" type="integer" value="0" label="trim_left: Int" help="[default: 0] trim_left nucleotides are removed from the 5' end if trim_left is positive. Applied after trim_right and trunc_len."/> | |
46 <param name="identity" type="float" value="0.8" label="identity: Float" help="[default: 0.8] minimum combined primer match identity threshold."/> | |
47 <param name="min_length" type="integer" min="0" value="50" label="min_length: Int % Range(0, None)" help="[default: 50] Minimum amplicon length. Shorter amplicons are discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering."/> | |
48 <param name="max_length" type="integer" min="0" value="0" label="max_length: Int % Range(0, None)" help="[default: 0] Maximum amplicon length. Longer amplicons are discarded. Applied before trimming and truncation, so plan accordingly. Set to zero (default) to disable max length filtering."/> | |
49 <param name="n_jobs" type="integer" min="1" value="1" label="n_jobs: Int % Range(1, None)" help="[default: 1] Number of seperate processes to run."/> | |
50 <conditional name="__q2galaxy__GUI__conditional__batch_size__"> | |
51 <param name="__q2galaxy__GUI__select__" type="select" label="batch_size: Int % Range(1, None) | Str % Choices('auto')" help="[default: 'auto'] Number of sequences to process in a batch. The `auto` option is calculated from the number of sequences and number of jobs specified."> | |
52 <option value="auto" selected="true">auto (Str)</option> | |
53 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)">Provide a value (Int % Range(1, None))</option> | |
54 </param> | |
55 <when value="auto"> | |
56 <param name="batch_size" type="hidden" value="auto"/> | |
57 </when> | |
58 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)"> | |
59 <param name="batch_size" type="integer" min="1" value="" label="batch_size: Int % Range(1, None)" help="[required] Number of sequences to process in a batch. The `auto` option is calculated from the number of sequences and number of jobs specified."/> | |
60 </when> | |
61 </conditional> | |
62 <param name="read_orientation" type="select" label="read_orientation: Str % Choices('both', 'forward', 'reverse')" display="radio"> | |
63 <option value="both" selected="true">both</option> | |
64 <option value="forward">forward</option> | |
65 <option value="reverse">reverse</option> | |
66 </param> | |
67 </section> | |
68 </inputs> | |
69 <outputs> | |
70 <data name="reads" format="qza" label="${tool.name} on ${on_string}: reads.qza" from_work_dir="reads.qza"/> | |
71 </outputs> | |
72 <tests/> | |
73 <help> | |
74 QIIME 2: feature-classifier extract-reads | |
75 ========================================= | |
76 Extract reads from reference sequences. | |
77 | |
78 | |
79 Outputs: | |
80 -------- | |
81 :reads.qza: <no description> | |
82 | |
83 | | |
84 | |
85 Description: | |
86 ------------ | |
87 Extract simulated amplicon reads from a reference database. Performs in-silico PCR to extract simulated amplicons from reference sequences that match the input primer sequences (within the mismatch threshold specified by `identity`). Both primer sequences must be in the 5' -> 3' orientation. Sequences that fail to match both primers will be excluded. Reads are extracted, trimmed, and filtered in the following order: 1. reads are extracted in specified orientation; 2. primers are removed; 3. reads longer than `max_length` are removed; 4. reads are trimmed with `trim_right`; 5. reads are truncated to `trunc_len`; 6. reads are trimmed with `trim_left`; 7. reads shorter than `min_length` are removed. | |
88 | |
89 | |
90 | | |
91 | |
92 </help> | |
93 <citations> | |
94 <citation type="doi">10.1186/s40168-018-0470-z</citation> | |
95 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
96 </citations> | |
97 </tool> |