Mercurial > repos > q2d2 > qiime2__quality_filter__q_score
changeset 0:8bf2383917c3 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter commit 9023cfd83495a517fbcbb6f91d5b01a6f1afcda1
author | q2d2 |
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date | Mon, 29 Aug 2022 20:22:53 +0000 |
parents | |
children | 2c4de53c8903 |
files | qiime2__quality_filter__q_score.xml test-data/.gitkeep |
diffstat | 1 files changed, 68 insertions(+), 0 deletions(-) [+] |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/qiime2__quality_filter__q_score.xml Mon Aug 29 20:22:53 2022 +0000 @@ -0,0 +1,68 @@ +<?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 quality-filter q-score" id="qiime2__quality_filter__q_score" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause"> + <description>Quality filter based on sequence quality scores.</description> + <requirements> + <container type="docker">quay.io/qiime2/core:2022.8</container> + </requirements> + <version_command>q2galaxy version quality_filter</version_command> + <command detect_errors="aggressive">q2galaxy run quality_filter q_score '$inputs'</command> + <configfiles> + <inputs name="inputs" data_style="paths"/> + </configfiles> + <inputs> + <param name="demux" type="data" format="qza" label="demux: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]¹ | SampleData[JoinedSequencesWithQuality]²" help="[required] The demultiplexed sequence data to be quality filtered."> + <options options_filter_attribute="metadata.semantic_type"> + <filter type="add_value" value="SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]"/> + <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/> + </options> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]']</validator> + </param> + <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options"> + <param name="min_quality" type="integer" value="4" label="min_quality: Int" help="[default: 4] The minimum acceptable PHRED score. All PHRED scores less that this value are considered to be low PHRED scores."/> + <param name="quality_window" type="integer" value="3" label="quality_window: Int" help="[default: 3] The maximum number of low PHRED scores that can be observed in direct succession before truncating a sequence read."/> + <param name="min_length_fraction" type="float" value="0.75" label="min_length_fraction: Float" help="[default: 0.75] The minimum length that a sequence read can be following truncation and still be retained. This length should be provided as a fraction of the input sequence length."/> + <param name="max_ambiguous" type="integer" value="0" label="max_ambiguous: Int" help="[default: 0] The maximum number of ambiguous (i.e., N) base calls. This is applied after trimming sequences based on `min_length_fraction`."/> + </section> + </inputs> + <outputs> + <data name="filtered_sequences" format="qza" label="${tool.name} on ${on_string}: filtered_sequences.qza" from_work_dir="filtered_sequences.qza"/> + <data name="filter_stats" format="qza" label="${tool.name} on ${on_string}: filter_stats.qza" from_work_dir="filter_stats.qza"/> + </outputs> + <tests/> + <help> +QIIME 2: quality-filter q-score +=============================== +Quality filter based on sequence quality scores. + + +Outputs: +-------- +:filtered_sequences.qza: The resulting quality-filtered sequences. +:filter_stats.qza: Summary statistics of the filtering process. + +| + +Description: +------------ +This method filters sequence based on quality scores and the presence of ambiguous base calls. + + +| + +</help> + <citations> + <citation type="doi">10.1038/nmeth.2276</citation> + <citation type="doi">10.1038/s41587-019-0209-9</citation> + </citations> +</tool>