Mercurial > repos > q2d2 > qiime2__rescript__degap_seqs
comparison qiime2__rescript__degap_seqs.xml @ 0:e5e634e9d13d draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__rescript commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
| author | q2d2 |
|---|---|
| date | Thu, 25 Apr 2024 21:23:07 +0000 |
| parents | |
| children | 2d1063325be1 |
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| -1:000000000000 | 0:e5e634e9d13d |
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| 1 <?xml version='1.0' encoding='utf-8'?> | |
| 2 <!-- | |
| 3 Copyright (c) 2024, 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: 2024.2.1) | |
| 10 for: | |
| 11 qiime2 (version: 2024.2.0) | |
| 12 --> | |
| 13 <tool name="qiime2 rescript degap-seqs" id="qiime2__rescript__degap_seqs" version="2024.2.2+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause"> | |
| 14 <description>Remove gaps from DNA sequence alignments.</description> | |
| 15 <requirements> | |
| 16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container> | |
| 17 </requirements> | |
| 18 <version_command>q2galaxy version rescript</version_command> | |
| 19 <command detect_errors="exit_code">q2galaxy run rescript degap_seqs '$inputs'</command> | |
| 20 <configfiles> | |
| 21 <inputs name="inputs" data_style="staging_path_and_source_path"/> | |
| 22 </configfiles> | |
| 23 <inputs> | |
| 24 <param name="aligned_sequences" type="data" format="qza" label="aligned_sequences: FeatureData[AlignedSequence]" help="[required] Aligned DNA Sequences to be degapped."> | |
| 25 <options options_filter_attribute="metadata.semantic_type"> | |
| 26 <filter type="add_value" value="FeatureData[AlignedSequence]"/> | |
| 27 </options> | |
| 28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[AlignedSequence]']</validator> | |
| 29 </param> | |
| 30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
| 31 <param name="min_length" type="integer" min="1" value="1" label="min_length: Int % Range(1, None)" help="[default: 1] Minimum length of sequence to be returned after degapping."/> | |
| 32 </section> | |
| 33 </inputs> | |
| 34 <outputs> | |
| 35 <data name="degapped_sequences" format="qza" label="${tool.name} on ${on_string}: degapped_sequences.qza" from_work_dir="degapped_sequences.qza"/> | |
| 36 </outputs> | |
| 37 <tests/> | |
| 38 <help> | |
| 39 QIIME 2: rescript degap-seqs | |
| 40 ============================ | |
| 41 Remove gaps from DNA sequence alignments. | |
| 42 | |
| 43 | |
| 44 Outputs: | |
| 45 -------- | |
| 46 :degapped_sequences.qza: The resulting unaligned (degapped) DNA sequences. | |
| 47 | |
| 48 | | |
| 49 | |
| 50 Description: | |
| 51 ------------ | |
| 52 This method converts aligned DNA sequences to unaligned DNA sequences by removing gaps ("-") and missing data (".") characters from the sequences. Essentially, 'unaligning' the sequences. | |
| 53 | |
| 54 | |
| 55 | | |
| 56 | |
| 57 </help> | |
| 58 <citations> | |
| 59 <citation type="doi">10.1371/journal.pcbi.1009581</citation> | |
| 60 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
| 61 </citations> | |
| 62 </tool> |