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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"
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3 version="2020.8">
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4 <description>Demultiplex paired-end sequence data with barcodes in- sequence.</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 cutadapt demux-paired
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10
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11 --i-seqs=$iseqs
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12 # if $input_files_mforwardbarcodesfile:
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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-forward-barcodes-file=' + d['additional_input'].__getattr__('file_name')
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17 # end for
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18 # return $file_list
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19 # end def
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20 --m-forward-barcodes-file=$list_dict_to_string($input_files_mforwardbarcodesfile)
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21 # end if
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22
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23 #if '__ob__' in str($mforwardbarcodescolumn):
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24 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__ob__', '[')
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25 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
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26 #end if
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27 #if '__cb__' in str($mforwardbarcodescolumn):
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28 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__cb__', ']')
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29 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
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30 #end if
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31 #if 'X' in str($mforwardbarcodescolumn):
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32 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('X', '\\')
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33 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
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34 #end if
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35 #if '__sq__' in str($mforwardbarcodescolumn):
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36 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__sq__', "'")
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37 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
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38 #end if
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39 #if '__db__' in str($mforwardbarcodescolumn):
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40 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__db__', '"')
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41 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
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42 #end if
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43
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44 --m-forward-barcodes-column=$mforwardbarcodescolumn
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45
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46 # if $input_files_mreversebarcodesfile:
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47 # def list_dict_to_string(list_dict):
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48 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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49 # for d in list_dict[1:]:
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50 # set $file_list = $file_list + ' --m-reverse-barcodes-file=' + d['additional_input'].__getattr__('file_name')
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51 # end for
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52 # return $file_list
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53 # end def
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54 --m-reverse-barcodes-file=$list_dict_to_string($input_files_mreversebarcodesfile)
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55 # end if
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56
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57 #if '__ob__' in str($mreversebarcodescolumn):
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58 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__ob__', '[')
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59 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
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60 #end if
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61 #if '__cb__' in str($mreversebarcodescolumn):
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62 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__cb__', ']')
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63 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
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64 #end if
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65 #if 'X' in str($mreversebarcodescolumn):
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66 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('X', '\\')
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67 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
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68 #end if
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69 #if '__sq__' in str($mreversebarcodescolumn):
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70 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__sq__', "'")
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71 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
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72 #end if
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73 #if '__db__' in str($mreversebarcodescolumn):
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74 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__db__', '"')
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75 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
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76 #end if
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77
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78 #if str($mreversebarcodescolumn):
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79 --m-reverse-barcodes-column=$mreversebarcodescolumn
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80 #end if
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81
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82 --p-error-rate=$perrorrate
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83
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84 --p-minimum-length=$pminimumlength
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85
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86 #if $pmixedorientation:
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87 --p-mixed-orientation
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88 #end if
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89
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90 --o-per-sample-sequences=opersamplesequences
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91
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92 --o-untrimmed-sequences=ountrimmedsequences
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93
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94 #if str($examples) != 'None':
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95 --examples=$examples
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96 #end if
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97
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98 ;
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99 cp ountrimmedsequences.qza $ountrimmedsequences
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100
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101 ]]></command>
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102 <inputs>
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103 <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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104 <repeat name="input_files_mforwardbarcodesfile" optional="True" title="--m-forward-barcodes-file">
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105 <param format="tabular,qza,no_unzip.zip" label="--m-forward-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
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106 </repeat>
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107 <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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108 <repeat name="input_files_mreversebarcodesfile" optional="True" title="--m-reverse-barcodes-file">
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109 <param format="tabular,qza,no_unzip.zip" label="--m-reverse-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
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110 </repeat>
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111 <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="False" type="text" />
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112 <param exclude_max="False" 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]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
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113 <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]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
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114 <param label="--p-mixed-orientation: --p-mixed-orientation: / --p-no-mixed-orientation Handle demultiplexing of mixed orientation reads (i.e. when forward and reverse reads coexist in the same file). [default: False]" name="pmixedorientation" selected="False" type="boolean" />
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115 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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116
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117 </inputs>
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118
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119 <outputs>
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120 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
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121 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences" />
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122
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123 </outputs>
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124
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125 <help><![CDATA[
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126 Demultiplex paired-end sequence data with barcodes in- sequence.
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127 ###############################################################
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128
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129 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
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130 are expected to be located within the sequence data (versus the header, or
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131 a separate barcode file).
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132
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133 Parameters
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134 ----------
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135 seqs : MultiplexedPairedEndBarcodeInSequence
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136 The paired-end sequences to be demultiplexed.
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137 forward_barcodes : MetadataColumn[Categorical]
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138 The sample metadata column listing the per-sample barcodes for the
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139 forward reads.
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140 reverse_barcodes : MetadataColumn[Categorical], optional
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141 The sample metadata column listing the per-sample barcodes for the
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142 reverse reads.
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143 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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144 The level of error tolerance, specified as the maximum allowable error
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145 rate.
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146 batch_size : Int % Range(0, None), optional
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147 The number of samples cutadapt demultiplexes concurrently.
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148 Demultiplexing in smaller batches will yield the same result with
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149 marginal speed loss, and may solve "too many files" errors related to
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150 sample quantity. Set to "0" to process all samples at once.
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151 minimum_length : Int % Range(1, None), optional
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152 Discard reads shorter than specified value. Note, the cutadapt default
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153 of 0 has been overridden, because that value produces empty sequence
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154 records.
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155 mixed_orientation : Bool, optional
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156 Handle demultiplexing of mixed orientation reads (i.e. when forward and
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157 reverse reads coexist in the same file).
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158
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159 Returns
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160 -------
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161 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
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162 The resulting demultiplexed sequences.
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163 untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
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164 The sequences that were unmatched to barcodes.
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165 ]]></help>
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166 <macros>
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167 <import>qiime_citation.xml</import>
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168 </macros>
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169 <expand macro="qiime_citation"/>
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170 </tool> |
