Mercurial > repos > q2d2 > qiime2__cutadapt__trim_single
diff qiime2__cutadapt__trim_single.xml @ 0:030225bdc91b draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
| author | q2d2 |
|---|---|
| date | Mon, 29 Aug 2022 19:22:32 +0000 |
| parents | |
| children | 1026d5863b7c |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__cutadapt__trim_single.xml Mon Aug 29 19:22:32 2022 +0000 @@ -0,0 +1,94 @@ +<?xml version='1.0' encoding='utf-8'?> +<!-- +Copyright (c) 2022, QIIME 2 development team. + +Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause) +--> +<!-- +This tool was automatically generated by: + q2galaxy (version: 2022.8.1) +for: + qiime2 (version: 2022.8.1) +--> +<tool name="qiime2 cutadapt trim-single" id="qiime2__cutadapt__trim_single" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Find and remove adapters in demultiplexed single-end sequences.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version cutadapt</version_command> + <command detect_errors="aggressive">q2galaxy run cutadapt trim_single '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="demultiplexed_sequences" type="data" format="qza" label="demultiplexed_sequences: SampleData[SequencesWithQuality]" help="[required] The single-end sequences to be trimmed."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="SampleData[SequencesWithQuality]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[SequencesWithQuality]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1] Number of CPU cores to use."/> + <repeat name="adapter" help="[optional] Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. 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: List[Str]"> + <param name="element" type="text" label="element: Str" help="[required]"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + </repeat> + <repeat name="front" 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." title="front: List[Str]"> + <param name="element" type="text" label="element: Str" help="[required]"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + </repeat> + <repeat name="anywhere" 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." title="anywhere: List[Str]"> + <param name="element" type="text" label="element: Str" help="[required]"> + <sanitizer> + <valid initial="string.printable"/> + </sanitizer> + <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator> + </param> + </repeat> + <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."/> + <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."/> + <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."/> + <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."/> + <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."/> + <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."/> + <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."/> + <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."/> + </section> + </inputs> + <outputs> + <data name="trimmed_sequences" format="qza" label="${tool.name} on ${on_string}: trimmed_sequences.qza" from_work_dir="trimmed_sequences.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: cutadapt trim-single +============================= +Find and remove adapters in demultiplexed single-end sequences. + + +Outputs: +-------- +:trimmed_sequences.qza: The resulting trimmed sequences. + +| + +Description: +------------ +Search demultiplexed single-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. + + +| + +</help> + <citations> + <citation type="doi">10.14806/ej.17.1.200</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>