Mercurial > repos > q2d2 > qiime2__quality_filter__q_score

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__quality_filter commit c7e80dcda727ce63b42aa8a946e9330310929797
author q2d2
date Mon, 03 Jun 2024 23:30:36 +0000
parents 1996c955a0e6
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1 <?xml version='1.0' encoding='utf-8'?>
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2 <!--
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3 Copyright (c) 2024, QIIME 2 development team.
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5 Distributed under the terms of the Modified BSD License. (SPDX: BSD-3-Clause)
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6 -->
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7 <!--
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8 This tool was automatically generated by:
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9 q2galaxy (version: 2024.5.0)
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10 for:
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11 qiime2 (version: 2024.5.0)
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12 -->
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13 <tool name="qiime2 quality-filter q-score" id="qiime2__quality_filter__q_score" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Quality filter based on sequence quality scores.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.5</container>
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17 </requirements>
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18 <version_command>q2galaxy version quality_filter</version_command>
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19 <command detect_errors="exit_code">q2galaxy run quality_filter q_score '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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22 </configfiles>
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23 <inputs>
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24 <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.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="SampleData[SequencesWithQuality | PairedEndSequencesWithQuality]"/>
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27 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
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28 </options>
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29 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[JoinedSequencesWithQuality]', 'SampleData[PairedEndSequencesWithQuality]', 'SampleData[SequencesWithQuality]']</validator>
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30 </param>
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31 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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32 <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."/>
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33 <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."/>
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34 <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."/>
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35 <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`."/>
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36 </section>
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37 </inputs>
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38 <outputs>
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39 <data name="filtered_sequences" format="qza" label="${tool.name} on ${on_string}: filtered_sequences.qza" from_work_dir="filtered_sequences.qza"/>
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40 <data name="filter_stats" format="qza" label="${tool.name} on ${on_string}: filter_stats.qza" from_work_dir="filter_stats.qza"/>
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41 </outputs>
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42 <tests>
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43 <test>
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44 <param name="demux" value="q_score.test0.demuxed-seqs.qza" ftype="qza"/>
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45 <output name="filtered_sequences" ftype="qza">
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46 <assert_contents>
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47 <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">
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48 <has_line_matching expression="type: SampleData\[SequencesWithQuality\]"/>
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49 </has_archive_member>
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50 </assert_contents>
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51 </output>
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52 <output name="filter_stats" ftype="qza">
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53 <assert_contents>
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54 <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">
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55 <has_line_matching expression="type: QualityFilterStats"/>
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56 </has_archive_member>
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57 </assert_contents>
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58 </output>
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59 </test>
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60 </tests>
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61 <help>
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62 QIIME 2: quality-filter q-score
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63 ===============================
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64 Quality filter based on sequence quality scores.
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65
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67 Outputs:
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68 --------
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69 :filtered_sequences.qza: The resulting quality-filtered sequences.
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70 :filter_stats.qza: Summary statistics of the filtering process.
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72 |
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74 Description:
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75 ------------
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76 This method filters sequence based on quality scores and the presence of ambiguous base calls.
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77
1
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78 Examples:
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79 ---------
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80
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81 q_score
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82 *******
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83 Using the ``qiime2 quality-filter q-score`` tool:
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84 #. Set *"demux"* to ``#: demuxed-seqs.qza``
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85 #. Press the ``Execute`` button.
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86
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87 Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows:
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88 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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89
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90 .. list-table::
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91 :align: left
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92 :header-rows: 1
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93
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94 * - History Name
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95 - *"Name"* to set (be sure to press ``Save``)
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96 * - ``#: qiime2 quality-filter q-score [...] : filtered_sequences.qza``
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97 - ``dumux-filtered.qza``
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98 * - ``#: qiime2 quality-filter q-score [...] : filter_stats.qza``
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99 - ``demux-filter-stats.qza``
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100
0
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101
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102 |
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103
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104 </help>
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105 <citations>
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106 <citation type="doi">10.1038/nmeth.2276</citation>
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107 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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108 </citations>
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109 </tool>