Mercurial > repos > q2d2 > qiime2__cutadapt__trim_paired
comparison qiime2__cutadapt__trim_paired.xml @ 0:a3eb5e92ffb3 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
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| date | Mon, 29 Aug 2022 19:21:23 +0000 |
| parents | |
| children | 4f340404bbf8 |
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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 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> | |
| 14 <description>Find and remove adapters in demultiplexed paired-end sequences.</description> | |
| 15 <requirements> | |
| 16 <container type="docker">quay.io/qiime2/core:2022.8</container> | |
| 17 </requirements> | |
| 18 <version_command>q2galaxy version cutadapt</version_command> | |
| 19 <command detect_errors="aggressive">q2galaxy run cutadapt trim_paired '$inputs'</command> | |
| 20 <configfiles> | |
| 21 <inputs name="inputs" data_style="paths"/> | |
| 22 </configfiles> | |
| 23 <inputs> | |
| 24 <param name="demultiplexed_sequences" type="data" format="qza" label="demultiplexed_sequences: SampleData[PairedEndSequencesWithQuality]" help="[required] The paired-end sequences to be trimmed."> | |
| 25 <options options_filter_attribute="metadata.semantic_type"> | |
| 26 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/> | |
| 27 </options> | |
| 28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]']</validator> | |
| 29 </param> | |
| 30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> | |
| 31 <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1] Number of CPU cores to use."/> | |
| 32 <repeat name="adapter_f" help="[optional] Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in forward read. If your sequence of interest is "framed" by a 5' and a 3' adapter, use this parameter to define a "linked" primer - see https://cutadapt.readthedocs.io for complete details." title="adapter_f: List[Str]"> | |
| 33 <param name="element" type="text" label="element: Str" help="[required]"> | |
| 34 <sanitizer> | |
| 35 <valid initial="string.printable"/> | |
| 36 </sanitizer> | |
| 37 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> | |
| 38 </param> | |
| 39 </repeat> | |
| 40 <repeat name="front_f" help="[optional] Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in forward read." title="front_f: List[Str]"> | |
| 41 <param name="element" type="text" label="element: Str" help="[required]"> | |
| 42 <sanitizer> | |
| 43 <valid initial="string.printable"/> | |
| 44 </sanitizer> | |
| 45 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> | |
| 46 </param> | |
| 47 </repeat> | |
| 48 <repeat name="anywhere_f" help="[optional] Sequence of an adapter that may be ligated to the 5' or 3' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in forward read." title="anywhere_f: List[Str]"> | |
| 49 <param name="element" type="text" label="element: Str" help="[required]"> | |
| 50 <sanitizer> | |
| 51 <valid initial="string.printable"/> | |
| 52 </sanitizer> | |
| 53 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> | |
| 54 </param> | |
| 55 </repeat> | |
| 56 <repeat name="adapter_r" help="[optional] Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in reverse read. If your sequence of interest is "framed" by a 5' and a 3' adapter, use this parameter to define a "linked" primer - see https://cutadapt.readthedocs.io for complete details." title="adapter_r: List[Str]"> | |
| 57 <param name="element" type="text" label="element: Str" help="[required]"> | |
| 58 <sanitizer> | |
| 59 <valid initial="string.printable"/> | |
| 60 </sanitizer> | |
| 61 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> | |
| 62 </param> | |
| 63 </repeat> | |
| 64 <repeat name="front_r" help="[optional] Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in reverse read." title="front_r: List[Str]"> | |
| 65 <param name="element" type="text" label="element: Str" help="[required]"> | |
| 66 <sanitizer> | |
| 67 <valid initial="string.printable"/> | |
| 68 </sanitizer> | |
| 69 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> | |
| 70 </param> | |
| 71 </repeat> | |
| 72 <repeat name="anywhere_r" help="[optional] Sequence of an adapter that may be ligated to the 5' or 3' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in reverse read." title="anywhere_r: List[Str]"> | |
| 73 <param name="element" type="text" label="element: Str" help="[required]"> | |
| 74 <sanitizer> | |
| 75 <valid initial="string.printable"/> | |
| 76 </sanitizer> | |
| 77 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> | |
| 78 </param> | |
| 79 </repeat> | |
| 80 <param name="error_rate" type="float" min="0" max="1" value="0.1" label="error_rate: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.1] Maximum allowed error rate."/> | |
| 81 <param name="indels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="indels: Bool" help="[default: Yes] Allow insertions or deletions of bases when matching adapters."/> | |
| 82 <param name="times" type="integer" min="1" value="1" label="times: Int % Range(1, None)" help="[default: 1] Remove multiple occurrences of an adapter if it is repeated, up to `times` times."/> | |
| 83 <param name="overlap" type="integer" min="1" value="3" label="overlap: Int % Range(1, None)" help="[default: 3] Require at least `overlap` bases of overlap between read and adapter for an adapter to be found."/> | |
| 84 <param name="match_read_wildcards" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="match_read_wildcards: Bool" help="[default: No] Interpret IUPAC wildcards (e.g., N) in reads."/> | |
| 85 <param name="match_adapter_wildcards" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="match_adapter_wildcards: Bool" help="[default: Yes] Interpret IUPAC wildcards (e.g., N) in adapters."/> | |
| 86 <param name="minimum_length" type="integer" min="1" value="1" label="minimum_length: Int % Range(1, None)" help="[default: 1] Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records."/> | |
| 87 <param name="discard_untrimmed" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="discard_untrimmed: Bool" help="[default: No] Discard reads in which no adapter was found."/> | |
| 88 </section> | |
| 89 </inputs> | |
| 90 <outputs> | |
| 91 <data name="trimmed_sequences" format="qza" label="${tool.name} on ${on_string}: trimmed_sequences.qza" from_work_dir="trimmed_sequences.qza"/> | |
| 92 </outputs> | |
| 93 <tests/> | |
| 94 <help> | |
| 95 QIIME 2: cutadapt trim-paired | |
| 96 ============================= | |
| 97 Find and remove adapters in demultiplexed paired-end sequences. | |
| 98 | |
| 99 | |
| 100 Outputs: | |
| 101 -------- | |
| 102 :trimmed_sequences.qza: The resulting trimmed sequences. | |
| 103 | |
| 104 | | |
| 105 | |
| 106 Description: | |
| 107 ------------ | |
| 108 Search demultiplexed paired-end sequences for adapters and remove them. The parameter descriptions in this method are adapted from the official cutadapt docs - please see those docs at https://cutadapt.readthedocs.io for complete details. | |
| 109 | |
| 110 | |
| 111 | | |
| 112 | |
| 113 </help> | |
| 114 <citations> | |
| 115 <citation type="doi">10.14806/ej.17.1.200</citation> | |
| 116 <citation type="doi">10.1038/s41587-019-0209-9</citation> | |
| 117 </citations> | |
| 118 </tool> |