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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="2018.4">
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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="2018.4">qiime2</requirement>
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6 </requirements>
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7 <command><![CDATA[
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8
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9 qiime cutadapt demux-paired --i-seqs=$iseqs
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10
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11 #def list_dict_to_string(list_dict):
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12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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13 #for d in list_dict[1:]:
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14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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15 #end for
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16 #return $file_list
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17 #end def
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18
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19 --m-forward-barcodes-file=$list_dict_to_string($input_files_mforwardbarcodesfile) --m-forward-barcodes-column="$mforwardbarcodescolumn"
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20
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21 #if str($cmdconfig) != 'None':
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22 --cmd-config=$cmdconfig
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23 #end if
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24
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25 --o-per-sample-sequences=opersamplesequences --o-untrimmed-sequences=ountrimmedsequences
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26
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27 #if $perrorrate:
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28 --p-error-rate=$perrorrate
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29 #end if
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30 ;
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31
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32 cp opersamplesequences.qza $opersamplesequences;
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33 cp ountrimmedsequences.qza $ountrimmedsequences;
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34
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35 ]]></command>
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36 <inputs>
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37 <param format="qza,no_unzip.zip" label="--i-seqs: Multiplexed Paired End Barcode In Sequence - The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
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38 <repeat name="input_files_mforwardbarcodesfile" optional="False" title="--m-forward-barcodes-file">
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39 <param label="--m-forward-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
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40 </repeat>
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41 <param label="--m-forward-barcodes-column: Metadata Column[Categorical] - Column from metadata file or artifact viewable as metadata. The sample metadata column listing the per-sample barcodes for the forward reads. [required]" name="mforwardbarcodescolumn" optional="False" type="text"/>
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42 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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43 <param label="--p-error-rate: The level of error tolerance, specified as the maximum allowable error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" value="0.1"/>
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44 </inputs>
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45 <outputs>
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46 <data format="qza" label="${tool.name} on ${on_string}: per-sample-sequences.qza" name="opersamplesequences"/>
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47 <data format="qza" label="${tool.name} on ${on_string}: untrimmed-sequences.qza" name="ountrimmedsequences"/>
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48 </outputs>
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49 <help><![CDATA[
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50
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51 Demultiplex paired-end sequence data with barcodes in-sequence.
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52 ---------------------------------------------------------------
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53
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54 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
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55 are expected to be located within the sequence data (versus the header, or
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56 a separate barcode file).
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57
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58 Parameters
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59 ----------
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60 seqs : MultiplexedPairedEndBarcodeInSequence
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61 The paired-end sequences to be demultiplexed.
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62 forward_barcodes : MetadataColumn[Categorical]
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63 The sample metadata column listing the per-sample barcodes for the
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64 forward reads.
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65 error_rate : Float % Range(0, 1, inclusive_end=True), optional
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66 The level of error tolerance, specified as the maximum allowable error
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67 rate.
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68
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69 Returns
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70 -------
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71 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
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72 The resulting demultiplexed sequences.
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73 untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
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74 The sequences that were unmatched to barcodes.
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75
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76 ]]>
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77 </help>
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78 </tool>
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