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Changeset 0:a3eb5e92ffb3 (2022-08-29)

Next changeset 1:4f340404bbf8 (2023-01-13)

Commit message:
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__cutadapt commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1

added:
qiime2__cutadapt__trim_paired.xml
test-data/.gitkeep

diff -r 000000000000 -r a3eb5e92ffb3 qiime2__cutadapt__trim_paired.xml
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/qiime2__cutadapt__trim_paired.xml Mon Aug 29 19:21:23 2022 +0000

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b'@@ -0,0 +1,118 @@\n+<?xml version=\'1.0\' encoding=\'utf-8\'?>\n+\n+\n+<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">\n+ <description>Find and remove adapters in demultiplexed paired-end sequences.</description>\n+ <requirements>\n+ <container type="docker">quay.io/qiime2/core:2022.8</container>\n+ </requirements>\n+ <version_command>q2galaxy version cutadapt</version_command>\n+ <command detect_errors="aggressive">q2galaxy run cutadapt trim_paired \'$inputs\'</command>\n+ <configfiles>\n+ <inputs name="inputs" data_style="paths"/>\n+ </configfiles>\n+ <inputs>\n+ <param name="demultiplexed_sequences" type="data" format="qza" label="demultiplexed_sequences: SampleData[PairedEndSequencesWithQuality]" help="[required] The paired-end sequences to be trimmed.">\n+ <options options_filter_attribute="metadata.semantic_type">\n+ <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>\n+ </options>\n+ <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in [\'SampleData[PairedEndSequencesWithQuality]\']</validator>\n+ </param>\n+ <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">\n+ <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1] Number of CPU cores to use."/>\n+ <repeat name="adapter_f" help="[optional] Sequence of an adapter ligated to the 3\' end. The adapter and any subsequent bases are trimmed. If a `$` 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]">\n+ <param name="element" type="text" label="element: Str" help="[required]">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator>\n+ </param>\n+ </repeat>\n+ <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]">\n+ <param name="element" type="text" label="element: Str" help="[required]">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator>\n+ </param>\n+ </repeat>\n+ <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]">\n+ <param '..b'le"/>\n+ </sanitizer>\n+ <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator>\n+ </param>\n+ </repeat>\n+ <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]">\n+ <param name="element" type="text" label="element: Str" help="[required]">\n+ <sanitizer>\n+ <valid initial="string.printable"/>\n+ </sanitizer>\n+ <validator type="expression" message="Please verify this parameter.">value is not None and len(value) > 0</validator>\n+ </param>\n+ </repeat>\n+ <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."/>\n+ <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."/>\n+ <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."/>\n+ <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."/>\n+ <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."/>\n+ <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."/>\n+ <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."/>\n+ <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."/>\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="trimmed_sequences" format="qza" label="${tool.name} on ${on_string}: trimmed_sequences.qza" from_work_dir="trimmed_sequences.qza"/>\n+ </outputs>\n+ <tests/>\n+ <help>\n+QIIME 2: cutadapt trim-paired\n+=============================\n+Find and remove adapters in demultiplexed paired-end sequences.\n+\n+\n+Outputs:\n+--------\n+:trimmed_sequences.qza: The resulting trimmed sequences.\n+\n+| \n+\n+Description:\n+------------\n+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.\n+\n+\n+| \n+\n+</help>\n+ <citations>\n+ <citation type="doi">10.14806/ej.17.1.200</citation>\n+ <citation type="doi">10.1038/s41587-019-0209-9</citation>\n+ </citations>\n+</tool>\n'