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comparison qiime2/qiime_demux_emp-single.xml @ 2:149432539226 draft

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author florianbegusch
date Wed, 17 Jul 2019 01:49:31 -0400
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1:6851c25d84b7 2:149432539226
1 <?xml version="1.0" ?>
2 <tool id="qiime_demux_emp-single" name="qiime demux emp-single" version="2019.4">
3 <description> - Demultiplex sequence data generated with the EMP protocol.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime demux emp-single
9
10 --i-seqs=$iseqs
11 --m-barcodes-column="$mbarcodescolumn"
12
13
14 #def list_dict_to_string(list_dict):
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
16 #for d in list_dict[1:]:
17 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
18 #end for
19 #return $file_list
20 #end def
21
22 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
23
24
25 #if $pnogolayerrorcorrection:
26 --p-no-golay-error-correction
27 #end if
28
29 #if $prevcompbarcodes:
30 --p-rev-comp-barcodes
31 #end if
32
33 #if $prevcompmappingbarcodes:
34 --p-rev-comp-mapping-barcodes
35 #end if
36
37 --o-per-sample-sequences=opersamplesequences
38 --o-error-correction-details=oerrorcorrectiondetails
39 ;
40 cp opersamplesequences.qza $opersamplesequences;
41 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
42 ]]></command>
43 <inputs>
44 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
45 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip"/>
46 </repeat>
47
48 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT RawSequences | EMPSingleEndSequences | EMPPairedEndSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
49 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
50 <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: False]" name="pnogolayerrorcorrection" selected="False" type="boolean"/>
51 <param label="--p-rev-comp-barcodes: --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean"/>
52 <param label="--p-rev-comp-mapping-barcodes: --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean"/>
53 </inputs>
54 <outputs>
55 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
56 <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails"/>
57 </outputs>
58 <help><![CDATA[
59 Demultiplex sequence data generated with the EMP protocol.
60 ##########################################################
61
62 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data
63 generated with the Earth Microbiome Project (EMP) amplicon sequencing
64 protocol. Details about this protocol can be found at
65 http://www.earthmicrobiome.org/protocols-and-standards/
66
67 Parameters
68 ----------
69 seqs : RawSequences | EMPSingleEndSequences | EMPPairedEndSequences
70 The single-end sequences to be demultiplexed.
71 barcodes : MetadataColumn[Categorical]
72 The sample metadata column containing the per-sample barcodes.
73 golay_error_correction : Bool, optional
74 Perform 12nt Golay error correction on the barcode reads.
75 rev_comp_barcodes : Bool, optional
76 If provided, the barcode sequence reads will be reverse complemented
77 prior to demultiplexing.
78 rev_comp_mapping_barcodes : Bool, optional
79 If provided, the barcode sequences in the sample metadata will be
80 reverse complemented prior to demultiplexing.
81
82 Returns
83 -------
84 per_sample_sequences : SampleData[SequencesWithQuality]
85 The resulting demultiplexed sequences.
86 error_correction_details : ErrorCorrectionDetails
87 Detail about the barcode error corrections.
88 ]]></help>
89 <macros>
90 <import>qiime_citation.xml</import>
91 </macros>
92 <expand macro="qiime_citation"/>
93 </tool>