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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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2
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11
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12 #def list_dict_to_string(list_dict):
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13 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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14 #for d in list_dict[1:]:
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15 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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16 #end for
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17 #return $file_list
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18 #end def
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19
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2
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20 #if $input_files_mforwardbarcodesfile:
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21 --m-forward-barcodes-file=$list_dict_to_string("$input_files_mforwardbarcodesfile")
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2
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22 #end if
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23
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24 #if $input_files_mreversebarcodesfile:
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25 --m-reverse-barcodes-file=$list_dict_to_string("$input_files_mreversebarcodesfile")
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2
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26 #end if
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27
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28 --m-forward-barcodes-column="$mforwardbarcodescolumn"
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29
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30 #if str($mreversebarcodescolumn):
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31 --m-reverse-barcodes-column="$mreversebarcodescolumn"
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32 #end if
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33
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34 #if $perrorrate:
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35 --p-error-rate=$perrorrate
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36 #end if
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37
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38
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39 --o-per-sample-sequences=opersamplesequences
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40 --o-untrimmed-sequences=ountrimmedsequences
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41 ;
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42
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43 cp opersamplesequences.qza $opersamplesequences;
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44 cp ountrimmedsequences.qza $ountrimmedsequences
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45 ]]></command>
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46 <inputs>
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47 <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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48 <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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49 <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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50
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51 <repeat name="input_files_mforwardbarcodesfile" optional="False" title="--m-forward-barcodes-file">
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52 <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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53 </repeat>
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54
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55 <repeat name="input_files_mreversebarcodesfile" optional="False" title="--m-reverse-barcodes-file">
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56 <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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57 </repeat>
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58
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59 <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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60 </inputs>
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61 <outputs>
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62 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
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63 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/>
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64 </outputs>
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65 <help><![CDATA[
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66 Demultiplex paired-end sequence data with barcodes in-sequence.
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67 ###############################################################
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68
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69 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
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70 are expected to be located within the sequence data (versus the header, or
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71 a separate barcode file).
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72
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73 Parameters
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74 ----------
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75 seqs : MultiplexedPairedEndBarcodeInSequence
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76 The paired-end sequences to be demultiplexed.
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77 forward_barcodes : MetadataColumn[Categorical]
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78 The sample metadata column listing the per-sample barcodes for the
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79 forward reads.
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80 reverse_barcodes : MetadataColumn[Categorical], optional
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81 The sample metadata column listing the per-sample barcodes for the
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82 reverse reads.
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83 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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84 The level of error tolerance, specified as the maximum allowable error
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85 rate.
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86
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87 Returns
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88 -------
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89 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
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90 The resulting demultiplexed sequences.
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91 untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
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92 The sequences that were unmatched to barcodes.
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93 ]]></help>
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94 <macros>
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95 <import>qiime_citation.xml</import>
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96 </macros>
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97 <expand macro="qiime_citation"/>
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98 </tool>
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