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1 <?xml version="1.0" ?>
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2 <tool id="qiime_demux_emp-single" name="qiime demux emp-single" version="2018.4">
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3 <description>- Demultiplex sequence data generated with the EMP protocol.</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 qiime demux emp-single --m-barcodes-column="$mbarcodescolumn" --i-seqs=$iseqs
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9
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10 #def list_dict_to_string(list_dict):
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11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
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12 #for d in list_dict[1:]:
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13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
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14 #end for
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15 #return $file_list
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16 #end def
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17
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18 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) --o-per-sample-sequences=opersamplesequences
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19
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20 #if $prevcompbarcodes:
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21 --p-rev-comp-barcodes
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22 #else
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23 --p-no-rev-comp-barcodes
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24 #end if
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25
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26 #if $prevcompmappingbarcodes:
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27 --p-rev-comp-mapping-barcodes
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28 #else
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29 --p-no-rev-comp-mapping-barcodes
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30 #end if
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31
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32 #if str($cmdconfig) != 'None':
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33 --cmd-config=$cmdconfig
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34 #end if
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35 ;
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36 cp opersamplesequences.qza $opersamplesequences;
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37 ]]></command>
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38 <inputs>
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39 <param format="qza,no_unzip.zip" label="--i-seqs: EMPPairedEndSequences | EMPSingleEndSequences | RawSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
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40 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
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41 <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"/>
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42 </repeat>
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43 <param label="--m-barcodes-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
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44 <param label="--p-rev-comp-barcodes: --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" checked="False" type="boolean"/>
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45 <param label="--p-rev-comp-mapping-barcodes: --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" checked="False" type="boolean"/>
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46 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
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47 </inputs>
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48 <outputs>
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49 <data format="qza" label="${tool.name} on ${on_string}: per-sample-sequences.qza" name="opersamplesequences"/>
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50 </outputs>
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51 <help><![CDATA[
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52 Demultiplex sequence data generated with the EMP protocol.
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53 ----------------------------------------------------------
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54
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55 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data
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56 generated with the Earth Microbiome Project (EMP) amplicon sequencing
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57 protocol. Details about this protocol can be found at
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58 http://www.earthmicrobiome.org/protocols-and-standards/
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59
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60 Parameters
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61 ----------
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62 seqs : EMPPairedEndSequences | EMPSingleEndSequences | RawSequences
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63 The single-end sequences to be demultiplexed.
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64 barcodes : MetadataColumn[Categorical]
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65 The sample metadata column containing the per-sample barcodes.
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66 rev_comp_barcodes : Bool, optional
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67 If provided, the barcode sequence reads will be reverse complemented
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68 prior to demultiplexing.
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69 rev_comp_mapping_barcodes : Bool, optional
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70 If provided, the barcode sequences in the sample metadata will be
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71 reverse complemented prior to demultiplexing.
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72
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73 Returns
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74 -------
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75 per_sample_sequences : SampleData[SequencesWithQuality]
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76 The resulting demultiplexed sequences.
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77 ]]>
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78 </help>
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79 <macros>
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80 <import>qiime_citation.xml</import>
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81 </macros>
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82 <expand macro="qiime_citation" />
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83 </tool>
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