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annotate qiime2__deblur__denoise_16S.xml @ 3:d2ba73cf503d draft

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planemo upload for repository https://github.com/qiime2/galaxy-tools/tree/main/tools/suite_qiime2__deblur commit 389df0134cd0763dcf02aac6e623fc15f8861c1e
author q2d2
date Thu, 25 Apr 2024 20:54:54 +0000
parents b883cbea5623
children ab9ed5ac604c
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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: 2024.2.1)
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10 for:
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11 qiime2 (version: 2024.2.0)
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12 -->
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13 <tool name="qiime2 deblur denoise-16S" id="qiime2__deblur__denoise_16S" version="2024.2.0+q2galaxy.2024.2.1" profile="22.05" license="BSD-3-Clause">
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14 <description>Deblur sequences using a 16S positive filter.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/amplicon:2024.2</container>
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17 </requirements>
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18 <version_command>q2galaxy version deblur</version_command>
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19 <command detect_errors="exit_code">q2galaxy run deblur denoise_16S '$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="demultiplexed_seqs" type="data" format="qza" label="demultiplexed_seqs: SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]" help="[required] The demultiplexed sequences to be denoised.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
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27 <filter type="add_value" value="SampleData[JoinedSequencesWithQuality]"/>
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28 <filter type="add_value" value="SampleData[SequencesWithQuality]"/>
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29 </options>
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30 <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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31 </param>
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32 <param name="trim_length" type="integer" value="" label="trim_length: Int" help="[required] Sequence trim length, specify -1 to disable trimming."/>
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33 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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34 <param name="left_trim_len" type="integer" min="0" value="0" label="left_trim_len: Int % Range(0, None)" help="[default: 0] Sequence trimming from the 5' end. A value of 0 will disable this trim."/>
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35 <param name="sample_stats" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="sample_stats: Bool" help="[default: No] If true, gather stats per sample."/>
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36 <param name="mean_error" type="float" value="0.005" label="mean_error: Float" help="[default: 0.005] The mean per nucleotide error, used for original sequence estimate."/>
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37 <param name="indel_prob" type="float" value="0.01" label="indel_prob: Float" help="[default: 0.01] Insertion/deletion (indel) probability (same for N indels)."/>
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38 <param name="indel_max" type="integer" value="3" label="indel_max: Int" help="[default: 3] Maximum number of insertion/deletions."/>
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39 <param name="min_reads" type="integer" value="10" label="min_reads: Int" help="[default: 10] Retain only features appearing at least min_reads times across all samples in the resulting feature table."/>
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40 <param name="min_size" type="integer" value="2" label="min_size: Int" help="[default: 2] In each sample, discard all features with an abundance less than min_size."/>
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41 <param name="hashed_feature_ids" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="hashed_feature_ids: Bool" help="[default: Yes] If true, hash the feature IDs."/>
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42 </section>
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43 </inputs>
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44 <outputs>
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45 <data name="table" format="qza" label="${tool.name} on ${on_string}: table.qza" from_work_dir="table.qza"/>
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46 <data name="representative_sequences" format="qza" label="${tool.name} on ${on_string}: representative_sequences.qza" from_work_dir="representative_sequences.qza"/>
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47 <data name="stats" format="qza" label="${tool.name} on ${on_string}: stats.qza" from_work_dir="stats.qza"/>
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48 </outputs>
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49 <tests>
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50 <test>
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51 <param name="demultiplexed_seqs" value="denoise_16S.test0.demux-filtered.qza" ftype="qza"/>
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52 <param name="trim_length" value="120"/>
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53 <param name="sample_stats" value="__q2galaxy__::literal::True"/>
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54 <output name="representative_sequences" ftype="qza">
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55 <assert_contents>
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56 <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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57 <has_line_matching expression="type: FeatureData\[Sequence\]"/>
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58 </has_archive_member>
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59 </assert_contents>
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60 </output>
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61 <output name="table" ftype="qza">
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62 <assert_contents>
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63 <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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64 <has_line_matching expression="type: FeatureTable\[Frequency\]"/>
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65 </has_archive_member>
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66 </assert_contents>
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67 </output>
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68 <output name="stats" ftype="qza">
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69 <assert_contents>
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70 <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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71 <has_line_matching expression="type: DeblurStats"/>
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72 </has_archive_member>
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73 </assert_contents>
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74 </output>
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75 </test>
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76 </tests>
0
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77 <help>
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78 QIIME 2: deblur denoise-16S
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79 ===========================
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80 Deblur sequences using a 16S positive filter.
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81
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82
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83 Outputs:
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84 --------
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85 :table.qza: The resulting denoised feature table.
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86 :representative_sequences.qza: The resulting feature sequences.
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87 :stats.qza: Per-sample stats if requested.
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88
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89 |
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90
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91 Description:
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92 ------------
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93 Perform sequence quality control for Illumina data using the Deblur workflow with a 16S reference as a positive filter. Only forward reads are supported at this time. The specific reference used is the 88% OTUs from Greengenes 13_8. This mode of operation should only be used when data were generated from a 16S amplicon protocol on an Illumina platform. The reference is only used to assess whether each sequence is likely to be 16S by a local alignment using SortMeRNA with a permissive e-value; the reference is not used to characterize the sequences.
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94
1
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95 Examples:
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96 ---------
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97
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98 denoise_16S
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99 ***********
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100 Using the ``qiime2 deblur denoise-16S`` tool:
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101 #. Set *"demultiplexed_seqs"* to ``#: demux-filtered.qza``
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102 #. Set *"trim_length"* to ``120``
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103 #. Expand the ``additional options`` section
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104
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105 - Set *"sample_stats"* to ``Yes``
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106
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107 #. Press the ``Execute`` button.
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108
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109 Once completed, for each new entry in your history, use the ``Edit`` button to set the name as follows:
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110 (Renaming is optional, but it will make any subsequent steps easier to complete.)
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111
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112 .. list-table::
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113 :align: left
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114 :header-rows: 1
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115
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116 * - History Name
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117 - *"Name"* to set (be sure to press ``Save``)
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118 * - ``#: qiime2 deblur denoise-16S [...] : table.qza``
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119 - ``table.qza``
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120 * - ``#: qiime2 deblur denoise-16S [...] : representative_sequences.qza``
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121 - ``representative-sequences.qza``
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122 * - ``#: qiime2 deblur denoise-16S [...] : stats.qza``
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123 - ``denoising-stats.qza``
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124
0
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125
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126 |
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127
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128 </help>
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129 <citations>
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130 <citation type="bibtex">@article{cite1,
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131 author = {Amir, Amnon and McDonald, Daniel and Navas-Molina, Jose A and Kopylova, Evguenia and Morton, James T and Xu, Zhenjiang Zech and Kightley, Eric P and Thompson, Luke R and Hyde, Embriette R and Gonzalez, Antonio and Knight, Rob},
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132 journal = {MSystems},
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133 number = {2},
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134 pages = {e00191--16},
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135 publisher = {Am Soc Microbiol},
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136 title = {Deblur rapidly resolves single-nucleotide community sequence patterns},
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137 volume = {2},
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138 year = {2017}
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139 }
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140 </citation>
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141 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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142 </citations>
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143 </tool>