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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"
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3 version="2020.8">
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4 <description>Demultiplex paired-end sequence data generated with the EMP protocol.</description>
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5 <requirements>
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6 <requirement type="package" version="2020.8">qiime2</requirement>
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7 </requirements>
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8 <command><![CDATA[
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9 qiime demux emp-paired
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10
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11 --i-seqs=$iseqs
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12 # if $input_files_mbarcodesfile:
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13 # def list_dict_to_string(list_dict):
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14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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15 # for d in list_dict[1:]:
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16 # set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name')
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17 # end for
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18 # return $file_list
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19 # end def
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20 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
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21 # end if
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22
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23 #if '__ob__' in str($mbarcodescolumn):
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24 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[')
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25 #set $mbarcodescolumn = $mbarcodescolumn_temp
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26 #end if
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27 #if '__cb__' in str($mbarcodescolumn):
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28 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']')
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29 #set $mbarcodescolumn = $mbarcodescolumn_temp
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30 #end if
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31 #if 'X' in str($mbarcodescolumn):
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32 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\')
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33 #set $mbarcodescolumn = $mbarcodescolumn_temp
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34 #end if
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35 #if '__sq__' in str($mbarcodescolumn):
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36 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
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37 #set $mbarcodescolumn = $mbarcodescolumn_temp
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38 #end if
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39 #if '__db__' in str($mbarcodescolumn):
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40 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"')
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41 #set $mbarcodescolumn = $mbarcodescolumn_temp
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42 #end if
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43
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44 --m-barcodes-column=$mbarcodescolumn
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45
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46
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47 #if $pnogolayerrorcorrection:
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48 --p-no-golay-error-correction
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49 #end if
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50
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51 #if $prevcompbarcodes:
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52 --p-rev-comp-barcodes
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53 #end if
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54
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55 #if $prevcompmappingbarcodes:
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56 --p-rev-comp-mapping-barcodes
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57 #end if
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58
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59 --o-per-sample-sequences=opersamplesequences
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60
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61 --o-error-correction-details=oerrorcorrectiondetails
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62
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63 #if str($examples) != 'None':
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64 --examples=$examples
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65 #end if
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66
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67 ;
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68 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
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69
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70 ]]></command>
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71 <inputs>
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72 <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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73 <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
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74 <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
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75 </repeat>
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76 <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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77 <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" />
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78 <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --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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79 <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --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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80 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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81
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82 </inputs>
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83
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84 <outputs>
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85 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
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86 <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails" />
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87
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88 </outputs>
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89
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90 <help><![CDATA[
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91 Demultiplex paired-end sequence data generated with the EMP protocol.
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92 ###############################################################
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93
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94 Demultiplex paired-end sequence data (i.e., map barcode reads to sample
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95 ids) for data generated with the Earth Microbiome Project (EMP) amplicon
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96 sequencing protocol. Details about this protocol can be found at
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97 http://www.earthmicrobiome.org/protocols-and-standards/
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98
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99 Parameters
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100 ----------
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101 seqs : EMPPairedEndSequences
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102 The paired-end sequences to be demultiplexed.
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103 barcodes : MetadataColumn[Categorical]
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104 The sample metadata column containing the per-sample barcodes.
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105 golay_error_correction : Bool, optional
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106 Perform 12nt Golay error correction on the barcode reads.
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107 rev_comp_barcodes : Bool, optional
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108 If provided, the barcode sequence reads will be reverse complemented
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109 prior to demultiplexing.
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110 rev_comp_mapping_barcodes : Bool, optional
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111 If provided, the barcode sequences in the sample metadata will be
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112 reverse complemented prior to demultiplexing.
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113
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114 Returns
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115 -------
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116 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
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117 The resulting demultiplexed sequences.
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118 error_correction_details : ErrorCorrectionDetails
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119 Detail about the barcode error corrections.
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120 ]]></help>
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121 <macros>
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122 <import>qiime_citation.xml</import>
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123 </macros>
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124 <expand macro="qiime_citation"/>
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125 </tool> |
