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1 <?xml version="1.0" ?>
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2 <tool id="qiime_demux_emp-paired" name="qiime demux emp-paired" version="2019.4">
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3 <description> - Demultiplex paired-end sequence data generated with the EMP protocol.</description>
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4 <requirements>
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5 <requirement type="package" version="2019.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8 qiime demux emp-paired
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9
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10 --i-seqs=$iseqs
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11 --m-barcodes-column="$mbarcodescolumn"
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12
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13
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14 #def list_dict_to_string(list_dict):
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15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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16 #for d in list_dict[1:]:
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17 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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18 #end for
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19 #return $file_list
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20 #end def
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21
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22 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
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23
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24
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25 #if $pnogolayerrorcorrection:
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26 --p-no-golay-error-correction
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27 #end if
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28
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29 #if $prevcompbarcodes:
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30 --p-rev-comp-barcodes
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31 #end if
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32
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33 #if $prevcompmappingbarcodes:
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34 --p-rev-comp-mapping-barcodes
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35 #end if
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36
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37 --o-per-sample-sequences=opersamplesequences
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38 --o-error-correction-details=oerrorcorrectiondetails
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39 ;
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40 cp opersamplesequences.qza $opersamplesequences;
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41 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
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42 ]]></command>
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43 <inputs>
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44 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
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45 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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46 </repeat>
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47 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT EMPPairedEndSequences The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
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48 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
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49 <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: False]" name="pnogolayerrorcorrection" selected="False" type="boolean"/>
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50 <param label="--p-rev-comp-barcodes: --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean"/>
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51 <param label="--p-rev-comp-mapping-barcodes: --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean"/>
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52 </inputs>
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53 <outputs>
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54 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
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55 <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails"/>
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56 </outputs>
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57 <help><![CDATA[
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58 Demultiplex paired-end sequence data generated with the EMP protocol.
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59 #####################################################################
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60
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61 Demultiplex paired-end sequence data (i.e., map barcode reads to sample
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62 ids) for data generated with the Earth Microbiome Project (EMP) amplicon
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63 sequencing protocol. Details about this protocol can be found at
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64 http://www.earthmicrobiome.org/protocols-and-standards/
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65
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66 Parameters
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67 ----------
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68 seqs : EMPPairedEndSequences
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69 The paired-end sequences to be demultiplexed.
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70 barcodes : MetadataColumn[Categorical]
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71 The sample metadata column containing the per-sample barcodes.
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72 golay_error_correction : Bool, optional
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73 Perform 12nt Golay error correction on the barcode reads.
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74 rev_comp_barcodes : Bool, optional
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75 If provided, the barcode sequence reads will be reverse complemented
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76 prior to demultiplexing.
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77 rev_comp_mapping_barcodes : Bool, optional
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78 If provided, the barcode sequences in the sample metadata will be
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79 reverse complemented prior to demultiplexing.
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80
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81 Returns
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82 -------
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83 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
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84 The resulting demultiplexed sequences.
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85 error_correction_details : ErrorCorrectionDetails
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86 Detail about the barcode error corrections.
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87 ]]></help>
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88 <macros>
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89 <import>qiime_citation.xml</import>
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90 </macros>
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91 <expand macro="qiime_citation"/>
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92 </tool>
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