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