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