Mercurial > repos > q2d2 > qiime2__cutadapt__trim_paired

annotate qiime2__cutadapt__trim_paired.xml @ 0:a3eb5e92ffb3 draft

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author q2d2
date Mon, 29 Aug 2022 19:21:23 +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) 2022, QIIME 2 development team.
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4
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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: 2022.8.1)
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10 for:
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11 qiime2 (version: 2022.8.1)
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12 -->
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13 <tool name="qiime2 cutadapt trim-paired" id="qiime2__cutadapt__trim_paired" version="2022.8.0+q2galaxy.2022.8.1.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Find and remove adapters in demultiplexed paired-end sequences.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2022.8</container>
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17 </requirements>
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18 <version_command>q2galaxy version cutadapt</version_command>
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19 <command detect_errors="aggressive">q2galaxy run cutadapt trim_paired '$inputs'</command>
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20 <configfiles>
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21 <inputs name="inputs" data_style="paths"/>
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22 </configfiles>
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23 <inputs>
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24 <param name="demultiplexed_sequences" type="data" format="qza" label="demultiplexed_sequences: SampleData[PairedEndSequencesWithQuality]" help="[required] The paired-end sequences to be trimmed.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="SampleData[PairedEndSequencesWithQuality]"/>
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27 </options>
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28 <validator type="expression" message="Incompatible type">hasattr(value.metadata, "semantic_type") and value.metadata.semantic_type in ['SampleData[PairedEndSequencesWithQuality]']</validator>
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29 </param>
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30 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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31 <param name="cores" type="integer" min="1" value="1" label="cores: Int % Range(1, None)" help="[default: 1] Number of CPU cores to use."/>
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32 <repeat name="adapter_f" help="[optional] Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in forward read. If your sequence of interest is &quot;framed&quot; by a 5' and a 3' adapter, use this parameter to define a &quot;linked&quot; primer - see https://cutadapt.readthedocs.io for complete details." title="adapter_f: List[Str]">
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33 <param name="element" type="text" label="element: Str" help="[required]">
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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 </repeat>
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40 <repeat name="front_f" help="[optional] Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in forward read." title="front_f: List[Str]">
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41 <param name="element" type="text" label="element: Str" help="[required]">
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42 <sanitizer>
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43 <valid initial="string.printable"/>
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44 </sanitizer>
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45 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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46 </param>
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47 </repeat>
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48 <repeat name="anywhere_f" help="[optional] Sequence of an adapter that may be ligated to the 5' or 3' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in forward read." title="anywhere_f: List[Str]">
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49 <param name="element" type="text" label="element: Str" help="[required]">
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50 <sanitizer>
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51 <valid initial="string.printable"/>
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52 </sanitizer>
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53 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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54 </param>
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55 </repeat>
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56 <repeat name="adapter_r" help="[optional] Sequence of an adapter ligated to the 3' end. The adapter and any subsequent bases are trimmed. If a `$` is appended, the adapter is only found if it is at the end of the read. Search in reverse read. If your sequence of interest is &quot;framed&quot; by a 5' and a 3' adapter, use this parameter to define a &quot;linked&quot; primer - see https://cutadapt.readthedocs.io for complete details." title="adapter_r: List[Str]">
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57 <param name="element" type="text" label="element: Str" help="[required]">
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58 <sanitizer>
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59 <valid initial="string.printable"/>
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60 </sanitizer>
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61 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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62 </param>
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63 </repeat>
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64 <repeat name="front_r" help="[optional] Sequence of an adapter ligated to the 5' end. The adapter and any preceding bases are trimmed. Partial matches at the 5' end are allowed. If a `^` character is prepended, the adapter is only found if it is at the beginning of the read. Search in reverse read." title="front_r: List[Str]">
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65 <param name="element" type="text" label="element: Str" help="[required]">
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66 <sanitizer>
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67 <valid initial="string.printable"/>
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68 </sanitizer>
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69 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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70 </param>
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71 </repeat>
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72 <repeat name="anywhere_r" help="[optional] Sequence of an adapter that may be ligated to the 5' or 3' end. Both types of matches as described under `adapter` and `front` are allowed. If the first base of the read is part of the match, the behavior is as with `front`, otherwise as with `adapter`. This option is mostly for rescuing failed library preparations - do not use if you know which end your adapter was ligated to. Search in reverse read." title="anywhere_r: List[Str]">
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73 <param name="element" type="text" label="element: Str" help="[required]">
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74 <sanitizer>
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75 <valid initial="string.printable"/>
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76 </sanitizer>
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77 <validator type="expression" message="Please verify this parameter.">value is not None and len(value) &gt; 0</validator>
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78 </param>
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79 </repeat>
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80 <param name="error_rate" type="float" min="0" max="1" value="0.1" label="error_rate: Float % Range(0, 1, inclusive_end=True)" help="[default: 0.1] Maximum allowed error rate."/>
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81 <param name="indels" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="indels: Bool" help="[default: Yes] Allow insertions or deletions of bases when matching adapters."/>
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82 <param name="times" type="integer" min="1" value="1" label="times: Int % Range(1, None)" help="[default: 1] Remove multiple occurrences of an adapter if it is repeated, up to `times` times."/>
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83 <param name="overlap" type="integer" min="1" value="3" label="overlap: Int % Range(1, None)" help="[default: 3] Require at least `overlap` bases of overlap between read and adapter for an adapter to be found."/>
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84 <param name="match_read_wildcards" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="match_read_wildcards: Bool" help="[default: No] Interpret IUPAC wildcards (e.g., N) in reads."/>
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85 <param name="match_adapter_wildcards" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" checked="true" label="match_adapter_wildcards: Bool" help="[default: Yes] Interpret IUPAC wildcards (e.g., N) in adapters."/>
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86 <param name="minimum_length" type="integer" min="1" value="1" label="minimum_length: Int % Range(1, None)" help="[default: 1] Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records."/>
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87 <param name="discard_untrimmed" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="discard_untrimmed: Bool" help="[default: No] Discard reads in which no adapter was found."/>
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88 </section>
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89 </inputs>
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90 <outputs>
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91 <data name="trimmed_sequences" format="qza" label="${tool.name} on ${on_string}: trimmed_sequences.qza" from_work_dir="trimmed_sequences.qza"/>
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92 </outputs>
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93 <tests/>
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94 <help>
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95 QIIME 2: cutadapt trim-paired
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96 =============================
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97 Find and remove adapters in demultiplexed paired-end sequences.
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98
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99
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100 Outputs:
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101 --------
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102 :trimmed_sequences.qza: The resulting trimmed sequences.
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103
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104 |
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105
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106 Description:
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107 ------------
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108 Search demultiplexed paired-end sequences for adapters and remove them. The parameter descriptions in this method are adapted from the official cutadapt docs - please see those docs at https://cutadapt.readthedocs.io for complete details.
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109
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110
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111 |
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112
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113 </help>
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114 <citations>
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115 <citation type="doi">10.14806/ej.17.1.200</citation>
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116 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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117 </citations>
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118 </tool>