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1 <?xml version="1.0" ?>
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2 <tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired" version="2019.4">
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3 <description> - Demultiplex paired-end sequence data with barcodes in- sequence.</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 cutadapt demux-paired
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9 --i-seqs=$iseqs
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10
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4
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11
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12 #if $input_files_mforwardbarcodesfile:
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13 #def list_dict_to_string_forward(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 + ',' + d['additional_input'].__getattr__('file_name')
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17 #end for
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18 #return $file_list
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19 #end def
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20 --m-forward-barcodes-file=$list_dict_to_string_forward($input_files_mforwardbarcodesfile)
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21 #end if
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22
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23 #if $input_files_mreversebarcodesfile:
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24 #def list_dict_to_string_reverse(list_dict):
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25 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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26 #for d in list_dict[1:]:
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27 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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28 #end for
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29 #return $file_list
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2
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30 #end def
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4
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31 --m-reverse-barcodes-file=$list_dict_to_string_reverse($input_files_mreversebarcodesfile)
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32 #end if
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2
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33
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4
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34
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35
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36
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37 #if '__sq__' in str($mforwardbarcodescolumn):
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38 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__sq__', "'")
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39 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
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40 #end if
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41
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42 #if '__db__' in str($mforwardbarcodescolumn):
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43 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__db__', '"')
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44 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
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45 #end if
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2
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46
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4
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47 #if str($mforwardbarcodescolumn):
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2
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48 --m-forward-barcodes-column="$mforwardbarcodescolumn"
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4
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49 #end if
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50
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51
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52
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53
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54 #if '__sq__' in str($mreversebarcodescolumn):
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55 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__sq__', "'")
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56 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
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57 #end if
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58
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59 #if '__db__' in str($mreversebarcodescolumn):
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60 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__db__', '"')
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61 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
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62 #end if
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2
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63
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64 #if str($mreversebarcodescolumn):
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65 --m-reverse-barcodes-column="$mreversebarcodescolumn"
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66 #end if
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67
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4
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68
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69
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2
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70 #if $perrorrate:
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71 --p-error-rate=$perrorrate
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72 #end if
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73
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74
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4
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75
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2
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76 --o-per-sample-sequences=opersamplesequences
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77 --o-untrimmed-sequences=ountrimmedsequences
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78 ;
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79
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80 cp opersamplesequences.qza $opersamplesequences;
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81 cp ountrimmedsequences.qza $ountrimmedsequences
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82 ]]></command>
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83 <inputs>
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84 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedPairedEndBarcodeInSequence The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
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85 <param label="--m-forward-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the forward reads. [required]" name="mforwardbarcodescolumn" optional="False" type="text"/>
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86 <param label="--m-reverse-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the reverse reads. [optional]" name="mreversebarcodescolumn" optional="True" type="text"/>
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87
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88 <repeat name="input_files_mforwardbarcodesfile" optional="False" title="--m-forward-barcodes-file">
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89 <param label="--m-forward-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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90 </repeat>
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91
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92 <repeat name="input_files_mreversebarcodesfile" optional="False" title="--m-reverse-barcodes-file">
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93 <param label="--m-reverse-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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94 </repeat>
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95
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96 <param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/>
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97 </inputs>
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98 <outputs>
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99 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
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100 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/>
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101 </outputs>
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102 <help><![CDATA[
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103 Demultiplex paired-end sequence data with barcodes in-sequence.
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104 ###############################################################
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105
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106 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
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107 are expected to be located within the sequence data (versus the header, or
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108 a separate barcode file).
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109
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110 Parameters
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111 ----------
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112 seqs : MultiplexedPairedEndBarcodeInSequence
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113 The paired-end sequences to be demultiplexed.
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114 forward_barcodes : MetadataColumn[Categorical]
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115 The sample metadata column listing the per-sample barcodes for the
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116 forward reads.
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117 reverse_barcodes : MetadataColumn[Categorical], optional
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118 The sample metadata column listing the per-sample barcodes for the
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119 reverse reads.
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120 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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121 The level of error tolerance, specified as the maximum allowable error
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122 rate.
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123
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124 Returns
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125 -------
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126 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
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127 The resulting demultiplexed sequences.
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128 untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
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129 The sequences that were unmatched to barcodes.
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130 ]]></help>
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131 <macros>
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132 <import>qiime_citation.xml</import>
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133 </macros>
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134 <expand macro="qiime_citation"/>
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135 </tool>
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