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author q2d2
date Wed, 30 Oct 2024 19:47:34 +0000
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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: 2024.10.0)
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10 for:
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11 qiime2 (version: 2024.10.1)
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12 -->
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13 <tool name="qiime2 feature-classifier extract-reads" id="qiime2__feature_classifier__extract_reads" version="2024.10.0+q2galaxy.2024.10.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Extract reads from reference sequences.</description>
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15 <xrefs>
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16 <xref type="bio.tools">qiime2</xref>
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17 </xrefs>
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18 <requirements>
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19 <container type="docker">quay.io/qiime2/amplicon:2024.10</container>
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20 </requirements>
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21 <version_command>q2galaxy version feature_classifier</version_command>
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22 <command detect_errors="exit_code">q2galaxy run feature_classifier extract_reads '$inputs'</command>
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23 <configfiles>
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24 <inputs name="inputs" data_style="staging_path_and_source_path"/>
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25 </configfiles>
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26 <inputs>
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27 <param name="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required]">
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28 <options options_filter_attribute="metadata.semantic_type">
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29 <filter type="add_value" value="FeatureData[Sequence]"/>
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30 </options>
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31 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
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32 </param>
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33 <param name="f_primer" type="text" label="f_primer: Str" help="[required] forward primer sequence (5' -&gt; 3').">
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34 <sanitizer>
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35 <valid initial="string.printable"/>
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36 </sanitizer>
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37 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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38 </param>
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39 <param name="r_primer" type="text" label="r_primer: Str" help="[required] reverse primer sequence (5' -&gt; 3'). Do not use reverse-complemented primer sequence.">
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40 <sanitizer>
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41 <valid initial="string.printable"/>
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42 </sanitizer>
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43 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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44 </param>
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45 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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46 <param name="trim_right" type="integer" value="0" label="trim_right: Int" help="[default: 0] trim_right nucleotides are removed from the 3' end if trim_right is positive. Applied before trunc_len and trim_left."/>
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47 <param name="trunc_len" type="integer" value="0" label="trunc_len: Int" help="[default: 0] read is cut to trunc_len if trunc_len is positive. Applied after trim_right but before trim_left."/>
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48 <param name="trim_left" type="integer" value="0" label="trim_left: Int" help="[default: 0] trim_left nucleotides are removed from the 5' end if trim_left is positive. Applied after trim_right and trunc_len."/>
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49 <param name="identity" type="float" value="0.8" label="identity: Float" help="[default: 0.8] minimum combined primer match identity threshold."/>
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50 <param name="min_length" type="integer" min="0" value="50" label="min_length: Int % Range(0, None)" help="[default: 50] Minimum amplicon length. Shorter amplicons are discarded. Applied after trimming and truncation, so be aware that trimming may impact sequence retention. Set to zero to disable min length filtering."/>
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51 <param name="max_length" type="integer" min="0" value="0" label="max_length: Int % Range(0, None)" help="[default: 0] Maximum amplicon length. Longer amplicons are discarded. Applied before trimming and truncation, so plan accordingly. Set to zero (default) to disable max length filtering."/>
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52 <param name="n_jobs" type="integer" min="1" value="1" label="n_jobs: Int % Range(1, None)" help="[default: 1] Number of seperate processes to run."/>
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53 <conditional name="__q2galaxy__GUI__conditional__batch_size__">
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54 <param name="__q2galaxy__GUI__select__" type="select" label="batch_size: Int % Range(1, None) | Str % Choices('auto')" help="[default: 'auto'] Number of sequences to process in a batch. The `auto` option is calculated from the number of sequences and number of jobs specified.">
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55 <option value="auto" selected="true">auto (Str)</option>
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56 <option value="__q2galaxy__::control::Int X Range(1__comma__ None)">Provide a value (Int % Range(1, None))</option>
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57 </param>
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58 <when value="auto">
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59 <param name="batch_size" type="hidden" value="auto"/>
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60 </when>
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61 <when value="__q2galaxy__::control::Int X Range(1__comma__ None)">
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62 <param name="batch_size" type="integer" min="1" value="" label="batch_size: Int % Range(1, None)" help="[required] Number of sequences to process in a batch. The `auto` option is calculated from the number of sequences and number of jobs specified."/>
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63 </when>
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64 </conditional>
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65 <param name="read_orientation" type="select" label="read_orientation: Str % Choices('both', 'forward', 'reverse')" display="radio">
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66 <option value="both" selected="true">both</option>
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67 <option value="forward">forward</option>
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68 <option value="reverse">reverse</option>
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69 </param>
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70 </section>
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71 </inputs>
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72 <outputs>
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73 <data name="reads" format="qza" label="${tool.name} on ${on_string}: reads.qza" from_work_dir="reads.qza"/>
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74 </outputs>
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75 <tests/>
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76 <help>
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77 QIIME 2: feature-classifier extract-reads
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78 =========================================
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79 Extract reads from reference sequences.
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80
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81
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82 Outputs:
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83 --------
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84 :reads.qza: &lt;no description&gt;
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85
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86 |
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87
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88 Description:
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89 ------------
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90 Extract simulated amplicon reads from a reference database. Performs in-silico PCR to extract simulated amplicons from reference sequences that match the input primer sequences (within the mismatch threshold specified by `identity`). Both primer sequences must be in the 5' -&gt; 3' orientation. Sequences that fail to match both primers will be excluded. Reads are extracted, trimmed, and filtered in the following order: 1. reads are extracted in specified orientation; 2. primers are removed; 3. reads longer than `max_length` are removed; 4. reads are trimmed with `trim_right`; 5. reads are truncated to `trunc_len`; 6. reads are trimmed with `trim_left`; 7. reads shorter than `min_length` are removed.
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91
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92
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93 |
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94
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95 </help>
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96 <citations>
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97 <citation type="doi">10.1186/s40168-018-0470-z</citation>
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98 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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99 </citations>
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100 </tool>