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comparison qiime2/qiime_demux_emp-single.xml @ 14:a0a8d77a991c draft

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author florianbegusch
date Thu, 03 Sep 2020 09:51:29 +0000
parents f190567fe3f6
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13:887cd4ad8e16 14:a0a8d77a991c
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_demux_emp-single" name="qiime demux emp-single" version="2019.7"> 2 <tool id="qiime_demux_emp-single" name="qiime demux emp-single"
3 <description> - Demultiplex sequence data generated with the EMP protocol.</description> 3 version="2020.8">
4 <requirements> 4 <description>Demultiplex sequence data generated with the EMP protocol.</description>
5 <requirement type="package" version="2019.7">qiime2</requirement> 5 <requirements>
6 </requirements> 6 <requirement type="package" version="2020.8">qiime2</requirement>
7 <command><![CDATA[ 7 </requirements>
8 <command><![CDATA[
8 qiime demux emp-single 9 qiime demux emp-single
9 10
10 --i-seqs=$iseqs 11 --i-seqs=$iseqs
11 --m-barcodes-column="$mbarcodescolumn" 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($input_files_mbarcodesfile)
21 # end if
12 22
23 #if '__ob__' in str($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
13 43
14 #if $input_files_mbarcodesfile: 44 --m-barcodes-column=$mbarcodescolumn
15 #def list_dict_to_string(list_dict):
16 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
17 #for d in list_dict[1:]:
18 #set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name')
19 #end for
20 #return $file_list
21 #end def
22 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
23 #end if
24 45
25 46
26 #if $pnogolayerrorcorrection: 47 #if $pnogolayerrorcorrection:
27 --p-no-golay-error-correction 48 --p-no-golay-error-correction
28 #end if 49 #end if
34 #if $prevcompmappingbarcodes: 55 #if $prevcompmappingbarcodes:
35 --p-rev-comp-mapping-barcodes 56 --p-rev-comp-mapping-barcodes
36 #end if 57 #end if
37 58
38 --o-per-sample-sequences=opersamplesequences 59 --o-per-sample-sequences=opersamplesequences
60
39 --o-error-correction-details=oerrorcorrectiondetails 61 --o-error-correction-details=oerrorcorrectiondetails
62
63 #if str($examples) != 'None':
64 --examples=$examples
65 #end if
66
40 ; 67 ;
41 cp opersamplesequences.qza $opersamplesequences;
42 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails 68 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
43 ]]></command>
44 <inputs>
45 <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file [optional]">
46 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [optional]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip"/>
47 </repeat>
48 69
49 <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"/> 70 ]]></command>
50 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/> 71 <inputs>
51 <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"/> 72 <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" />
52 <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"/> 73 <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
53 <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"/> 74 <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
54 </inputs> 75 </repeat>
55 <outputs> 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" />
56 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/> 77 <param label="--p-no-golay-error-correction: Do not perform 12nt Golay error correction on the barcode reads. [default: True]" name="pnogolayerrorcorrection" selected="False" type="boolean" />
57 <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails"/> 78 <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-barcodes: --p-rev-comp-barcodes: / --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" selected="False" type="boolean" />
58 </outputs> 79 <param format="tabular,qza,no_unzip.zip" label="--p-rev-comp-mapping-barcodes: --p-rev-comp-mapping-barcodes: / --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" selected="False" type="boolean" />
59 <help><![CDATA[ 80 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
81
82 </inputs>
83
84 <outputs>
85 <data format="qza" label="${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[
60 Demultiplex sequence data generated with the EMP protocol. 91 Demultiplex sequence data generated with the EMP protocol.
61 ########################################################## 92 ###############################################################
62 93
63 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data 94 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data
64 generated with the Earth Microbiome Project (EMP) amplicon sequencing 95 generated with the Earth Microbiome Project (EMP) amplicon sequencing
65 protocol. Details about this protocol can be found at 96 protocol. Details about this protocol can be found at
66 http://www.earthmicrobiome.org/protocols-and-standards/ 97 http://www.earthmicrobiome.org/protocols-and-standards/
84 ------- 115 -------
85 per_sample_sequences : SampleData[SequencesWithQuality] 116 per_sample_sequences : SampleData[SequencesWithQuality]
86 The resulting demultiplexed sequences. 117 The resulting demultiplexed sequences.
87 error_correction_details : ErrorCorrectionDetails 118 error_correction_details : ErrorCorrectionDetails
88 Detail about the barcode error corrections. 119 Detail about the barcode error corrections.
89 ]]></help> 120 ]]></help>
90 <macros> 121 <macros>
91 <import>qiime_citation.xml</import> 122 <import>qiime_citation.xml</import>
92 </macros> 123 </macros>
93 <expand macro="qiime_citation"/> 124 <expand macro="qiime_citation"/>
94 </tool> 125 </tool>