Mercurial > repos > q2d2 > qiime2__quality_control__exclude_seqs

comparison qiime2__quality_control__exclude_seqs.xml @ 0:7e3db22e1eaf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_control commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author q2d2
date Mon, 29 Aug 2022 20:20:21 +0000
parents
children f697a0b6a702
comparison
equal deleted inserted replaced
-1:000000000000 0:7e3db22e1eaf
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-control exclude-seqs" id="qiime2__quality_control__exclude_seqs" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
14 <description>Exclude sequences by alignment</description>
15 <requirements>
16 <container type="docker">quay.io/qiime2/core:2022.8</container>
17 </requirements>
18 <version_command>q2galaxy version quality_control</version_command>
19 <command detect_errors="aggressive">q2galaxy run quality_control exclude_seqs '$inputs'</command>
20 <configfiles>
21 <inputs name="inputs" data_style="paths"/>
22 </configfiles>
23 <inputs>
24 <param name="query_sequences" type="data" format="qza" label="query_sequences: FeatureData[Sequence]" help="[required] Sequences to test for exclusion">
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="reference_sequences" type="data" format="qza" label="reference_sequences: FeatureData[Sequence]" help="[required] Reference sequences to align against feature sequences">
31 <options options_filter_attribute="metadata.semantic_type">
32 <filter type="add_value" value="FeatureData[Sequence]"/>
33 </options>
34 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
35 </param>
36 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
37 <param name="method" type="select" label="method: Str % Choices('blast', 'blastn-short')¹ | Str % Choices('vsearch')²" help="[default: 'blast'] Alignment method to use for matching feature sequences against reference sequences">
38 <option value="blast" selected="true">blast (Str)</option>
39 <option value="blastn-short">blastn-short (Str)</option>
40 <option value="vsearch">vsearch (Str)</option>
41 </param>
42 <param name="perc_identity" type="float" min="0.0" max="1.0" value="0.97" label="perc_identity: Float % Range(0.0, 1.0, inclusive_end=True)" help="[default: 0.97] Reject match if percent identity to reference is lower. Must be in range [0.0, 1.0]"/>
43 <param name="evalue" type="float" optional="true" label="evalue: Float" help="[optional] BLAST expectation (E) value threshold for saving hits. Reject if E value is higher than threshold. This threshold is disabled by default."/>
44 <param name="perc_query_aligned" type="float" value="0.97" label="perc_query_aligned: Float" help="[default: 0.97] Percent of query sequence that must align to reference in order to be accepted as a hit."/>
45 <param name="threads" type="integer" min="1" value="1" label="threads: Int % Range(1, None)" help="[default: 1] Number of jobs to execute. Only applies to vsearch method."/>
46 <param name="left_justify" type="select" label="left_justify: Bool % Choices(False)¹ | Bool²" help="[default: No] Reject match if the pairwise alignment begins with gaps">
47 <option value="__q2galaxy__::literal::False" selected="true">No (Bool)</option>
48 <option value="__q2galaxy__::literal::True">Yes (Bool)</option>
49 </param>
50 </section>
51 </inputs>
52 <outputs>
53 <data name="sequence_hits" format="qza" label="${tool.name} on ${on_string}: sequence_hits.qza" from_work_dir="sequence_hits.qza"/>
54 <data name="sequence_misses" format="qza" label="${tool.name} on ${on_string}: sequence_misses.qza" from_work_dir="sequence_misses.qza"/>
55 </outputs>
56 <tests/>
57 <help>
58 QIIME 2: quality-control exclude-seqs
59 =====================================
60 Exclude sequences by alignment
61
62
63 Outputs:
64 --------
65 :sequence_hits.qza: Subset of feature sequences that align to reference sequences
66 :sequence_misses.qza: Subset of feature sequences that do not align to reference sequences
67
68 |
69
70 Description:
71 ------------
72 This method aligns feature sequences to a set of reference sequences to identify sequences that hit/miss the reference within a specified perc_identity, evalue, and perc_query_aligned. This method could be used to define a positive filter, e.g., extract only feature sequences that align to a certain clade of bacteria; or to define a negative filter, e.g., identify sequences that align to contaminant or human DNA sequences that should be excluded from subsequent analyses. Note that filtering is performed based on the perc_identity, perc_query_aligned, and evalue thresholds (the latter only if method==BLAST and an evalue is set). Set perc_identity==0 and/or perc_query_aligned==0 to disable these filtering thresholds as necessary.
73
74
75 |
76
77 </help>
78 <citations>
79 <citation type="doi">10.1186/1471-2105-10-421</citation>
80 <citation type="doi">10.1038/s41587-019-0209-9</citation>
81 </citations>
82 </tool>