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+ − 1 <?xml version="1.0" ?>
+ − 2 <tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single" version="2019.4">
+ − 3 <description> - Demultiplex single-end sequence data with barcodes in- sequence.</description>
+ − 4 <requirements>
+ − 5 <requirement type="package" version="2019.4">qiime2</requirement>
+ − 6 </requirements>
+ − 7 <command><![CDATA[
+ − 8 qiime cutadapt demux-single
+ − 9
+ − 10 --i-seqs=$iseqs
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+ − 11
+ − 12
+ − 13
+ − 14 #if '__sq__' in str($mbarcodescolumn):
+ − 15 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
+ − 16 #set $mbarcodescolumn = $mbarcodescolumn_temp
+ − 17 #end if
+ − 18
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+ − 19 --m-barcodes-column="$mbarcodescolumn"
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+ − 20
+ − 21
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+ − 22 --o-per-sample-sequences=opersamplesequences
+ − 23 --o-untrimmed-sequences=ountrimmedsequences
+ − 24
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+ − 25
+ − 26
+ − 27
+ − 28
+ − 29
+ − 30 #if $input_files_mbarcodesfile:
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+ − 31 #def list_dict_to_string(list_dict):
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+ − 32 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
+ − 33 #for d in list_dict[1:]:
+ − 34 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
+ − 35 #end for
+ − 36 #return $file_list
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+ − 37 #end def
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+ − 38 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
+ − 39 #end if
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+ − 40
+ − 41
+ − 42 #if $perrorrate:
+ − 43 --p-error-rate=$perrorrate
+ − 44 #end if
+ − 45
+ − 46 ;
+ − 47
+ − 48 cp opersamplesequences.qza $opersamplesequences;
+ − 49 cp ountrimmedsequences.qza $ountrimmedsequences
+ − 50 ]]></command>
+ − 51 <inputs>
+ − 52 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
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+ − 53 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
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+ − 54 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
+ − 55 </repeat>
+ − 56 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
+ − 57 <param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/>
+ − 58 </inputs>
+ − 59 <outputs>
+ − 60 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
+ − 61 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/>
+ − 62 </outputs>
+ − 63 <help><![CDATA[
+ − 64 Demultiplex single-end sequence data with barcodes in-sequence.
+ − 65 ###############################################################
+ − 66
+ − 67 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
+ − 68 are expected to be located within the sequence data (versus the header, or
+ − 69 a separate barcode file).
+ − 70
+ − 71 Parameters
+ − 72 ----------
+ − 73 seqs : MultiplexedSingleEndBarcodeInSequence
+ − 74 The single-end sequences to be demultiplexed.
+ − 75 barcodes : MetadataColumn[Categorical]
+ − 76 The sample metadata column listing the per-sample barcodes.
+ − 77 error_rate : Float % Range(0, 1, inclusive_end=True), optional
+ − 78 The level of error tolerance, specified as the maximum allowable error
+ − 79 rate. The default value specified by cutadapt is 0.1 (=10%), which is
+ − 80 greater than `demux emp-*`, which is 0.0 (=0%).
+ − 81
+ − 82 Returns
+ − 83 -------
+ − 84 per_sample_sequences : SampleData[SequencesWithQuality]
+ − 85 The resulting demultiplexed sequences.
+ − 86 untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence
+ − 87 The sequences that were unmatched to barcodes.
+ − 88 ]]></help>
+ − 89 <macros>
+ − 90 <import>qiime_citation.xml</import>
+ − 91 </macros>
+ − 92 <expand macro="qiime_citation"/>
+ − 93 </tool>
