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1 <?xml version="1.0" ?>
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2 <tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single"
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3 version="2020.8">
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4 <description>Demultiplex single-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-single
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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 --p-error-rate=$perrorrate
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48
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49 --p-minimum-length=$pminimumlength
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50
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51 --o-per-sample-sequences=opersamplesequences
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52
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53 --o-untrimmed-sequences=ountrimmedsequences
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54
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55 #if str($examples) != 'None':
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56 --examples=$examples
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57 #end if
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58
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59 ;
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60 cp ountrimmedsequences.qza $ountrimmedsequences
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61
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62 ]]></command>
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63 <inputs>
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64 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
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65 <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
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66 <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
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67 </repeat>
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68 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text" />
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69 <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. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
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70 <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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71 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
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72
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73 </inputs>
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74
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75 <outputs>
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76 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
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77 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences" />
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78
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79 </outputs>
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80
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81 <help><![CDATA[
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82 Demultiplex single-end sequence data with barcodes in- sequence.
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83 ###############################################################
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84
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85 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
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86 are expected to be located within the sequence data (versus the header, or
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87 a separate barcode file).
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88
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89 Parameters
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90 ----------
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91 seqs : MultiplexedSingleEndBarcodeInSequence
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92 The single-end sequences to be demultiplexed.
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93 barcodes : MetadataColumn[Categorical]
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94 The sample metadata column listing the per-sample barcodes.
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95 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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96 The level of error tolerance, specified as the maximum allowable error
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97 rate. The default value specified by cutadapt is 0.1 (=10%), which is
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98 greater than `demux emp-*`, which is 0.0 (=0%).
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99 batch_size : Int % Range(0, None), optional
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100 The number of samples cutadapt demultiplexes concurrently.
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101 Demultiplexing in smaller batches will yield the same result with
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102 marginal speed loss, and may solve "too many files" errors related to
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103 sample quantity. Set to "0" to process all samples at once.
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104 minimum_length : Int % Range(1, None), optional
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105 Discard reads shorter than specified value. Note, the cutadapt default
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106 of 0 has been overridden, because that value produces empty sequence
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107 records.
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108
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109 Returns
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110 -------
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111 per_sample_sequences : SampleData[SequencesWithQuality]
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112 The resulting demultiplexed sequences.
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113 untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence
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114 The sequences that were unmatched to barcodes.
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115 ]]></help>
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116 <macros>
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117 <import>qiime_citation.xml</import>
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118 </macros>
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119 <expand macro="qiime_citation"/>
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120 </tool> |
