Mercurial > repos > q2d2 > qiime2__rescript__orient_seqs

annotate qiime2__rescript__orient_seqs.xml @ 1:daf6c330ff82 draft

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author q2d2
date Mon, 03 Jun 2024 23:31:23 +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:
1
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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 rescript orient-seqs" id="qiime2__rescript__orient_seqs" version="2024.5.0+q2galaxy.2024.5.0" profile="22.05" license="BSD-3-Clause">
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14 <description>Orient input sequences by comparison against reference.</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 rescript</version_command>
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19 <command detect_errors="exit_code">q2galaxy run rescript orient_seqs '$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="sequences" type="data" format="qza" label="sequences: FeatureData[Sequence]" help="[required] Sequences to be oriented.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="FeatureData[Sequence]"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
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29 </param>
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30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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31 <param name="reference_sequences" type="data" format="qza" optional="true" label="reference_sequences: FeatureData[Sequence]" help="[optional] Reference sequences to orient against. If no reference is provided, all the sequences will be reverse complemented and all parameters will be ignored.">
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32 <options options_filter_attribute="metadata.semantic_type">
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33 <filter type="add_value" value="FeatureData[Sequence]"/>
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34 </options>
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35 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['FeatureData[Sequence]']</validator>
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36 </param>
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37 <param name="threads" type="integer" min="1" max="255" value="1" label="threads: Int % Range(1, 256)" help="[default: 1] Number of computation threads to use (1 to 256). The number of threads should be lesser or equal to the number of available CPU cores."/>
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38 <param name="dbmask" type="select" label="dbmask: Str % Choices('none', 'dust', 'soft')" display="radio">
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39 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
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40 <option value="none">none</option>
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41 <option value="dust">dust</option>
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42 <option value="soft">soft</option>
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43 </param>
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44 <conditional name="__q2galaxy__GUI__conditional__relabel__" label="relabel: Str">
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45 <param name="__q2galaxy__GUI__select__" type="select" label="relabel: Str" help="[optional] Relabel sequences using the prefix string and a ticker (1, 2, 3, etc.) to construct the new headers. Use --sizeout to conserve the abundance annotations.">
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46 <option value="__q2galaxy__::control::default" selected="true">None (Use default behavior)</option>
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47 <option value="__q2galaxy__::control::provide">Provide a value</option>
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48 </param>
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49 <when value="__q2galaxy__::control::default">
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50 <param name="relabel" type="hidden" value="__q2galaxy__::literal::None"/>
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51 </when>
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52 <when value="__q2galaxy__::control::provide">
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53 <param name="relabel" type="text">
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54 <sanitizer>
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55 <valid initial="string.printable"/>
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56 </sanitizer>
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57 </param>
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58 </when>
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59 </conditional>
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60 <param name="relabel_keep" type="select" label="relabel_keep: Bool" help="[optional] When relabeling, keep the original identifier in the header after a space." display="radio">
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61 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
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62 <option value="__q2galaxy__::literal::True">Yes</option>
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63 <option value="__q2galaxy__::literal::False">No</option>
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64 </param>
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65 <param name="relabel_md5" type="select" label="relabel_md5: Bool" help="[optional] When relabeling, use the MD5 digest of the sequence as the new identifier. Use --sizeout to conserve the abundance annotations." display="radio">
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66 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
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67 <option value="__q2galaxy__::literal::True">Yes</option>
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68 <option value="__q2galaxy__::literal::False">No</option>
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69 </param>
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70 <param name="relabel_self" type="select" label="relabel_self: Bool" help="[optional] Relabel sequences using the sequence itself as a label." display="radio">
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71 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
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72 <option value="__q2galaxy__::literal::True">Yes</option>
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73 <option value="__q2galaxy__::literal::False">No</option>
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74 </param>
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75 <param name="relabel_sha1" type="select" label="relabel_sha1: Bool" help="[optional] When relabeling, use the SHA1 digest of the sequence as the new identifier. The probability of a collision is smaller than the MD5 algorithm." display="radio">
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76 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
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77 <option value="__q2galaxy__::literal::True">Yes</option>
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78 <option value="__q2galaxy__::literal::False">No</option>
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79 </param>
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80 <param name="sizein" type="select" label="sizein: Bool" help="[optional] In de novo mode, abundance annotations (pattern `[&gt;;]size=integer[;]`) present in sequence headers are taken into account." display="radio">
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81 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
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82 <option value="__q2galaxy__::literal::True">Yes</option>
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83 <option value="__q2galaxy__::literal::False">No</option>
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84 </param>
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85 <param name="sizeout" type="select" label="sizeout: Bool" help="[optional] Add abundance annotations to the output FASTA files." display="radio">
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86 <option value="__q2galaxy__::literal::None" selected="true">None (Use default behavior)</option>
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87 <option value="__q2galaxy__::literal::True">Yes</option>
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88 <option value="__q2galaxy__::literal::False">No</option>
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89 </param>
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90 </section>
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91 </inputs>
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92 <outputs>
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93 <data name="oriented_seqs" format="qza" label="${tool.name} on ${on_string}: oriented_seqs.qza" from_work_dir="oriented_seqs.qza"/>
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94 <data name="unmatched_seqs" format="qza" label="${tool.name} on ${on_string}: unmatched_seqs.qza" from_work_dir="unmatched_seqs.qza"/>
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95 </outputs>
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96 <tests/>
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97 <help>
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98 QIIME 2: rescript orient-seqs
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99 =============================
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100 Orient input sequences by comparison against reference.
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101
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102
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103 Outputs:
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104 --------
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105 :oriented_seqs.qza: Query sequences in same orientation as top matching reference sequence.
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106 :unmatched_seqs.qza: Query sequences that fail to match at least one reference sequence in either + or - orientation. This will be empty if no refrence is provided.
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107
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108 |
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109
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110 Description:
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111 ------------
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112 Orient input sequences by comparison against a set of reference sequences using VSEARCH. This action can also be used to quickly filter out sequences that (do not) match a set of reference sequences in either orientation. Alternatively, if no reference sequences are provided as input, all input sequences will be reverse-complemented. In this case, no alignment is performed, and all alignment parameters (`dbmask`, `relabel`, `relabel_keep`, `relabel_md5`, `relabel_self`, `relabel_sha1`, `sizein`, `sizeout` and `threads`) are ignored.
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113
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114
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115 |
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116
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117 </help>
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118 <citations>
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119 <citation type="doi">10.7717/peerj.2584</citation>
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120 <citation type="doi">10.1371/journal.pcbi.1009581</citation>
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121 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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122 </citations>
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123 </tool>