Mercurial > repos > q2d2 > qiime2__cutadapt__demux_paired

annotate qiime2__cutadapt__demux_paired.xml @ 2:c6a8822e19f2 draft

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author q2d2
date Thu, 08 Jun 2023 19:34:55 +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) 2023, 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: 2023.5.0)
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10 for:
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11 qiime2 (version: 2023.5.1)
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12 -->
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13 <tool name="qiime2 cutadapt demux-paired" id="qiime2__cutadapt__demux_paired" version="2023.5.1+q2galaxy.2023.5.0.2" profile="22.05" license="BSD-3-Clause">
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14 <description>Demultiplex paired-end sequence data with barcodes in-sequence.</description>
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15 <requirements>
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16 <container type="docker">quay.io/qiime2/core:2023.5</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="exit_code">q2galaxy run cutadapt demux_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="seqs" type="data" format="qza" label="seqs: MultiplexedPairedEndBarcodeInSequence" help="[required] The paired-end sequences to be demultiplexed.">
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25 <options options_filter_attribute="metadata.semantic_type">
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26 <filter type="add_value" value="MultiplexedPairedEndBarcodeInSequence"/>
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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 ['MultiplexedPairedEndBarcodeInSequence']</validator>
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29 </param>
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30 <conditional name="forward_barcodes">
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31 <param name="type" type="select" label="forward_barcodes: MetadataColumn[Categorical]" help="[required] The sample metadata column listing the per-sample barcodes for the forward reads.">
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32 <option value="tsv" selected="true">Metadata from TSV</option>
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33 <option value="qza">Metadata from Artifact</option>
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34 </param>
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35 <when value="tsv">
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36 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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37 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
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38 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
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39 </param>
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40 </when>
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41 <when value="qza">
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42 <param name="source" type="data" format="qza" label="Metadata Source"/>
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43 <param name="column" type="text" label="Column Name">
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44 <validator type="empty_field"/>
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45 </param>
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46 </when>
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47 </conditional>
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48 <section name="__q2galaxy__GUI__section__extra_opts__" title="Click here for additional options">
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49 <conditional name="reverse_barcodes">
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50 <param name="type" type="select" label="reverse_barcodes: MetadataColumn[Categorical]" help="[optional] The sample metadata column listing the per-sample barcodes for the reverse reads.">
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51 <option value="none" selected="true">None (default)</option>
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52 <option value="tsv">Metadata from TSV</option>
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53 <option value="qza">Metadata from Artifact</option>
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54 </param>
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55 <when value="none"/>
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56 <when value="tsv">
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57 <param name="source" type="data" format="tabular,qiime2.tabular" label="Metadata Source"/>
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58 <param name="column" type="data_column" label="Column Name" data_ref="source" use_header_names="true">
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59 <validator type="expression" message="The first column cannot be selected (they are IDs).">value != "1"</validator>
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60 </param>
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61 </when>
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62 <when value="qza">
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63 <param name="source" type="data" format="qza" label="Metadata Source"/>
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64 <param name="column" type="text" label="Column Name">
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65 <validator type="empty_field"/>
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66 </param>
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67 </when>
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68 </conditional>
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69 <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] The level of error tolerance, specified as the maximum allowable error rate."/>
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70 <param name="batch_size" type="integer" min="0" value="0" label="batch_size: Int % Range(0, None)" help="[default: 0] The number of samples cutadapt demultiplexes concurrently. Demultiplexing in smaller batches will yield the same result with marginal speed loss, and may solve &quot;too many files&quot; errors related to sample quantity. Set to &quot;0&quot; to process all samples at once."/>
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71 <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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72 <param name="mixed_orientation" type="boolean" truevalue="__q2galaxy__::literal::True" falsevalue="__q2galaxy__::literal::False" label="mixed_orientation: Bool" help="[default: No] Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file)."/>
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73 <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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74 </section>
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75 </inputs>
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76 <outputs>
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77 <data name="per_sample_sequences" format="qza" label="${tool.name} on ${on_string}: per_sample_sequences.qza" from_work_dir="per_sample_sequences.qza"/>
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78 <data name="untrimmed_sequences" format="qza" label="${tool.name} on ${on_string}: untrimmed_sequences.qza" from_work_dir="untrimmed_sequences.qza"/>
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79 </outputs>
1
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80 <tests>
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81 <test>
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82 <param name="seqs" value="demux_paired.test0.seqs.qza" ftype="qza"/>
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83 <conditional name="forward_barcodes">
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84 <param name="type" value="tsv"/>
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85 <param name="source" value="demux_paired.test0.md.tsv" ftype="qiime2.tabular"/>
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86 <param name="column" value="2"/>
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87 </conditional>
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88 <output name="per_sample_sequences" ftype="qza">
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89 <assert_contents>
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90 <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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91 <has_line_matching expression="type: SampleData\[PairedEndSequencesWithQuality\]"/>
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92 </has_archive_member>
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93 </assert_contents>
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94 </output>
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95 <output name="untrimmed_sequences" ftype="qza">
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96 <assert_contents>
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97 <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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98 <has_line_matching expression="type: MultiplexedPairedEndBarcodeInSequence"/>
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99 </has_archive_member>
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100 </assert_contents>
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101 </output>
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102 </test>
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103 </tests>
0
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104 <help>
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105 QIIME 2: cutadapt demux-paired
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106 ==============================
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107 Demultiplex paired-end sequence data with barcodes in-sequence.
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108
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109
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110 Outputs:
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111 --------
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112 :per_sample_sequences.qza: The resulting demultiplexed sequences.
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113 :untrimmed_sequences.qza: The sequences that were unmatched to barcodes.
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114
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115 |
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116
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117 Description:
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118 ------------
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119 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes are expected to be located within the sequence data (versus the header, or a separate barcode file).
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120
1
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121 Examples:
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122 ---------
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123
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124 paired
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125 ******
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126 Using the ``qiime2 cutadapt demux-paired`` tool:
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127 #. Set *"seqs"* to ``#: seqs.qza``
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128 #. For *"forward_barcodes"*:
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129
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130 #. Leave as ``Metadata from TSV``
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131 #. Set *"Metadata Source"* to ``md.tsv``
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132 #. Set *"Column Name"* to ``barcode-sequence``
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133
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134 #. Press the ``Execute`` button.
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135
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136
0
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137
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138 |
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139
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140 </help>
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141 <citations>
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142 <citation type="doi">10.14806/ej.17.1.200</citation>
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143 <citation type="doi">10.1038/s41587-019-0209-9</citation>
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144 </citations>
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145 </tool>