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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="2019.7">
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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="2019.7">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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2
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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 + ' --m-forward-barcodes-file=' + d['additional_input'].__getattr__('file_name')
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4
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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 + ' --m-reverse-barcodes-file=' + d['additional_input'].__getattr__('file_name')
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28 #end for
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29 #return $file_list
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30 #end def
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31 --m-reverse-barcodes-file=$list_dict_to_string_reverse($input_files_mreversebarcodesfile)
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32 #end if
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33
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34
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35
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36 #if str($pbatchsize):
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37 --p-batch-size $pbatchsize
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38 #end if
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39
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40 #if str($pminimumlength):
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41 --p-minimum-length $pminimumlength
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42 #end if
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43
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44
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45
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46
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47 #if '__sq__' in str($mforwardbarcodescolumn):
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48 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__sq__', "'")
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49 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
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50 #end if
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51
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52 #if '__db__' in str($mforwardbarcodescolumn):
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53 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__db__', '"')
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54 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
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55 #end if
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56
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57
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58
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59
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60 #if '__sq__' in str($mreversebarcodescolumn):
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61 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__sq__', "'")
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62 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
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63 #end if
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64
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65 #if '__db__' in str($mreversebarcodescolumn):
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66 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__db__', '"')
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67 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
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68 #end if
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69
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70
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71
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72 #if str($mforwardbarcodescolumn):
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73 --m-forward-barcodes-column="$mforwardbarcodescolumn"
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74 #end if
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75
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76 #if str($mreversebarcodescolumn):
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77 --m-reverse-barcodes-column="$mreversebarcodescolumn"
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78 #end if
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79
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80
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81
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82 #if str($perrorrate):
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83 --p-error-rate=$perrorrate
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84 #end if
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85
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86
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87
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88 --o-per-sample-sequences=opersamplesequences
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89 --o-untrimmed-sequences=ountrimmedsequences
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90 ;
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91
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92 cp opersamplesequences.qza $opersamplesequences;
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93 cp ountrimmedsequences.qza $ountrimmedsequences
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94 ]]></command>
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95 <inputs>
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96
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97 <param label="--p-batch-size: INTEGER The number of samples cutadapt demultiplexes Range(0, None) concurrently. Demultiplexing in smaller batches will yield the same result with marginal speed loss, and may solve 'too many files' errors related to sample quantity. Set to '0' to process all samples at once. [default: 0]" name="pbatchsize" optional="True" type="integer" value="0" min="0"/>
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98 <param label="--p-minimum-length: INTEGER Range(1, None) Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" name="pminimumlength" optional="True" type="integer" value="1" min="1"/>
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99
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100
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101
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102 <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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103 <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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104 <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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105
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106 <repeat name="input_files_mforwardbarcodesfile" optional="False" title="--m-forward-barcodes-file">
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107 <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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108 </repeat>
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109
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110 <repeat name="input_files_mreversebarcodesfile" optional="False" title="--m-reverse-barcodes-file">
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111 <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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112 </repeat>
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113
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114 <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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115 </inputs>
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116 <outputs>
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117 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
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118 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/>
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119 </outputs>
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120 <help><![CDATA[
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121 Demultiplex paired-end sequence data with barcodes in-sequence.
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122 ################################################################
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123
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124 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
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125 are expected to be located within the sequence data (versus the header, or
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126 a separate barcode file).
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127
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128 Parameters
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129 ----------
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130 seqs : MultiplexedPairedEndBarcodeInSequence
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131 The paired-end sequences to be demultiplexed.
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132 forward_barcodes : MetadataColumn[Categorical]
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133 The sample metadata column listing the per-sample barcodes for the
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134 forward reads.
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135 reverse_barcodes : MetadataColumn[Categorical], optional
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136 The sample metadata column listing the per-sample barcodes for the
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137 reverse reads.
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138 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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139 The level of error tolerance, specified as the maximum allowable error
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140 rate.
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141 batch_size : Int % Range(0, None), optional
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142 The number of samples cutadapt demultiplexes concurrently.
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143 Demultiplexing in smaller batches will yield the same result with
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144 marginal speed loss, and may solve "too many files" errors related to
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145 sample quantity. Set to "0" to process all samples at once.
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146 minimum_length : Int % Range(1, None), optional
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147 Discard reads shorter than specified value. Note, the cutadapt default
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148 of 0 has been overridden, because that value produces empty sequence
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149 records.
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150
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151 Returns
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152 -------
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153 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
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154 The resulting demultiplexed sequences.
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155 untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
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156 The sequences that were unmatched to barcodes.
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157 ]]></help>
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158 <macros>
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159 <import>qiime_citation.xml</import>
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160 </macros>
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161 <expand macro="qiime_citation"/>
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162 </tool>
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