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comparison qiime2/qiime_demux_emp-paired.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_demux_emp-paired" name="qiime demux emp-paired"
3 version="2020.8">
4 <description>Demultiplex paired-end sequence data generated with the EMP protocol.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime demux emp-paired
10
11 --i-seqs=$iseqs
12 # if $input_files_mbarcodesfile:
13 # def list_dict_to_string(list_dict):
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 # for d in list_dict[1:]:
16 # set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
21 # end if
22
23 #if '__ob__' in str($mbarcodescolumn):
24 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[')
25 #set $mbarcodescolumn = $mbarcodescolumn_temp
26 #end if
27 #if '__cb__' in str($mbarcodescolumn):
28 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']')
29 #set $mbarcodescolumn = $mbarcodescolumn_temp
30 #end if
31 #if 'X' in str($mbarcodescolumn):
32 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\')
33 #set $mbarcodescolumn = $mbarcodescolumn_temp
34 #end if
35 #if '__sq__' in str($mbarcodescolumn):
36 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
37 #set $mbarcodescolumn = $mbarcodescolumn_temp
38 #end if
39 #if '__db__' in str($mbarcodescolumn):
40 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"')
41 #set $mbarcodescolumn = $mbarcodescolumn_temp
42 #end if
43
44 --m-barcodes-column=$mbarcodescolumn
45
46
47 #if $pnogolayerrorcorrection:
48 --p-no-golay-error-correction
49 #end if
50
51 #if $prevcompbarcodes:
52 --p-rev-comp-barcodes
53 #end if
54
55 #if $prevcompmappingbarcodes:
56 --p-rev-comp-mapping-barcodes
57 #end if
58
59 --o-per-sample-sequences=opersamplesequences
60
61 --o-error-correction-details=oerrorcorrectiondetails
62
63 #if str($examples) != 'None':
64 --examples=$examples
65 #end if
66
67 ;
68 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
69
70 ]]></command>
71 <inputs>
72 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT EMPPairedEndSequences The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
73 <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
74 <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
75 </repeat>
76 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text" />
77 <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" />
78 <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --p-rev-comp-barcodes: / --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean" />
79 <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --p-rev-comp-mapping-barcodes: / --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean" />
80 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
81
82 </inputs>
83
84 <outputs>
85 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
86 <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails" />
87
88 </outputs>
89
90 <help><![CDATA[
91 Demultiplex paired-end sequence data generated with the EMP protocol.
92 ###############################################################
93
94 Demultiplex paired-end sequence data (i.e., map barcode reads to sample
95 ids) for data generated with the Earth Microbiome Project (EMP) amplicon
96 sequencing protocol. Details about this protocol can be found at
97 http://www.earthmicrobiome.org/protocols-and-standards/
98
99 Parameters
100 ----------
101 seqs : EMPPairedEndSequences
102 The paired-end sequences to be demultiplexed.
103 barcodes : MetadataColumn[Categorical]
104 The sample metadata column containing the per-sample barcodes.
105 golay_error_correction : Bool, optional
106 Perform 12nt Golay error correction on the barcode reads.
107 rev_comp_barcodes : Bool, optional
108 If provided, the barcode sequence reads will be reverse complemented
109 prior to demultiplexing.
110 rev_comp_mapping_barcodes : Bool, optional
111 If provided, the barcode sequences in the sample metadata will be
112 reverse complemented prior to demultiplexing.
113
114 Returns
115 -------
116 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
117 The resulting demultiplexed sequences.
118 error_correction_details : ErrorCorrectionDetails
119 Detail about the barcode error corrections.
120 ]]></help>
121 <macros>
122 <import>qiime_citation.xml</import>
123 </macros>
124 <expand macro="qiime_citation"/>
125 </tool>