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comparison qiime2/qiime_demux_emp-paired.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_demux_emp-paired" name="qiime demux emp-paired" version="2019.4">
3 <description> - Demultiplex paired-end 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-paired
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 $oerrorcorrectiondetails
42 ]]></command>
43 <inputs>
44 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
45 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
46 </repeat>
47 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT EMPPairedEndSequences The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
48 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
49 <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: False]" name="pnogolayerrorcorrection" selected="False" type="boolean"/>
50 <param label="--p-rev-comp-barcodes: --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean"/>
51 <param label="--p-rev-comp-mapping-barcodes: --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean"/>
52 </inputs>
53 <outputs>
54 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
55 <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails"/>
56 </outputs>
57 <help><![CDATA[
58 Demultiplex paired-end sequence data generated with the EMP protocol.
59 #####################################################################
60
61 Demultiplex paired-end sequence data (i.e., map barcode reads to sample
62 ids) for data generated with the Earth Microbiome Project (EMP) amplicon
63 sequencing protocol. Details about this protocol can be found at
64 http://www.earthmicrobiome.org/protocols-and-standards/
65
66 Parameters
67 ----------
68 seqs : EMPPairedEndSequences
69 The paired-end sequences to be demultiplexed.
70 barcodes : MetadataColumn[Categorical]
71 The sample metadata column containing the per-sample barcodes.
72 golay_error_correction : Bool, optional
73 Perform 12nt Golay error correction on the barcode reads.
74 rev_comp_barcodes : Bool, optional
75 If provided, the barcode sequence reads will be reverse complemented
76 prior to demultiplexing.
77 rev_comp_mapping_barcodes : Bool, optional
78 If provided, the barcode sequences in the sample metadata will be
79 reverse complemented prior to demultiplexing.
80
81 Returns
82 -------
83 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
84 The resulting demultiplexed sequences.
85 error_correction_details : ErrorCorrectionDetails
86 Detail about the barcode error corrections.
87 ]]></help>
88 <macros>
89 <import>qiime_citation.xml</import>
90 </macros>
91 <expand macro="qiime_citation"/>
92 </tool>