Mercurial > repos > q2d2 > qiime2__quality_filter__q_score
changeset 1:2c4de53c8903 draft
planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter commit 69da7976573cc07a363ac66bdacc9269d7cd3732
author | q2d2 |
---|---|
date | Fri, 13 Jan 2023 22:59:48 +0000 |
parents | 8bf2383917c3 |
children | 090ca1116927 |
files | qiime2__quality_filter__q_score.xml test-data/.gitkeep test-data/q_score.test0.demuxed-seqs.qza |
diffstat | 2 files changed, 51 insertions(+), 9 deletions(-) [+] |
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--- a/qiime2__quality_filter__q_score.xml Mon Aug 29 20:22:53 2022 +0000 +++ b/qiime2__quality_filter__q_score.xml Fri Jan 13 22:59:48 2023 +0000 @@ -1,32 +1,33 @@ <?xml version='1.0' encoding='utf-8'?> <!-- -Copyright (c) 2022, QIIME 2 development team. +Copyright (c) 2023, 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) + q2galaxy (version: 2022.11.1) for: - qiime2 (version: 2022.8.1) + qiime2 (version: 2022.11.1) --> -<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"> +<tool name="qiime2 quality-filter q-score" id="qiime2__quality_filter__q_score" version="2022.11.1+q2galaxy.2022.11.1.2" 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> + <container type="docker">quay.io/qiime2/core:2022.11</container> </requirements> <version_command>q2galaxy version quality_filter</version_command> - <command detect_errors="aggressive">q2galaxy run quality_filter q_score '$inputs'</command> + <command detect_errors="exit_code">q2galaxy run quality_filter q_score '$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[SequencesWithQuality]"/> + <filter type="add_value" value="SampleData[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> + <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[SequencesWithQuality]', 'SampleData[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."/> @@ -39,7 +40,25 @@ <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/> + <tests> + <test> + <param name="demux" value="q_score.test0.demuxed-seqs.qza" ftype="qza"/> + <output name="filtered_sequences" ftype="qza"> + <assert_contents> + <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> + <has_line_matching expression="type: SampleData\[SequencesWithQuality\]"/> + </has_archive_member> + </assert_contents> + </output> + <output name="filter_stats" ftype="qza"> + <assert_contents> + <has_archive_member path="[0-9a-f]{8}-[0-9a-f]{4}-[4][0-9a-f]{3}-[89ab][0-9a-f]{3}-[0-9a-f]{12}\/metadata.yaml"> + <has_line_matching expression="type: QualityFilterStats"/> + </has_archive_member> + </assert_contents> + </output> + </test> + </tests> <help> QIIME 2: quality-filter q-score =============================== @@ -57,6 +76,29 @@ ------------ This method filters sequence based on quality scores and the presence of ambiguous base calls. +Examples: +--------- + +q_score +******* +Using the ``qiime2 quality-filter q-score`` tool: + #. Set *"demux"* to ``#: demuxed-seqs.qza`` + #. Press the ``Execute`` button. + +Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows: + (Renaming is optional, but it will make any subsequent steps easier to complete.) + + .. list-table:: + :align: left + :header-rows: 1 + + * - History Name + - *"Name"* to set (be sure to press ``Save``) + * - ``#: qiime2 quality-filter q-score [...] : filtered_sequences.qza`` + - ``dumux-filtered.qza`` + * - ``#: qiime2 quality-filter q-score [...] : filter_stats.qza`` + - ``demux-filter-stats.qza`` + |