annotate qiime2/qiime_demux_emp-paired.xml @ 1:255f48db74f8 draft

Hotfix
author florianbegusch
date Wed, 17 Jul 2019 03:26:16 -0400
parents 370e0b6e9826
children 51025741f326
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_demux_emp-paired" name="qiime demux emp-paired" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Demultiplex paired-end sequence data generated with the EMP protocol.</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime demux emp-paired
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-seqs=$iseqs
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --m-barcodes-column="$mbarcodescolumn"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 #def list_dict_to_string(list_dict):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16 #for d in list_dict[1:]:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 #end for
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 #return $file_list
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20 #end def
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 #if $pnogolayerrorcorrection:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 --p-no-golay-error-correction
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 #if $prevcompbarcodes:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 --p-rev-comp-barcodes
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 #if $prevcompmappingbarcodes:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 --p-rev-comp-mapping-barcodes
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 --o-per-sample-sequences=opersamplesequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 --o-error-correction-details=oerrorcorrectiondetails
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 cp opersamplesequences.qza $opersamplesequences;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41 cp oerrorcorrectiondetails.qza $oerrorcorrectiondetails
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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" />
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46 </repeat>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 <data format="qza" label="${tool.name} on ${on_string}: errorcorrectiondetails.qza" name="oerrorcorrectiondetails"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 Demultiplex paired-end sequence data generated with the EMP protocol.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 #####################################################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
60
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
61 Demultiplex paired-end sequence data (i.e., map barcode reads to sample
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
62 ids) for data generated with the Earth Microbiome Project (EMP) amplicon
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
63 sequencing protocol. Details about this protocol can be found at
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
64 http://www.earthmicrobiome.org/protocols-and-standards/
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
65
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
66 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 seqs : EMPPairedEndSequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 The paired-end sequences to be demultiplexed.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 barcodes : MetadataColumn[Categorical]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 The sample metadata column containing the per-sample barcodes.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
72 golay_error_correction : Bool, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
73 Perform 12nt Golay error correction on the barcode reads.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
74 rev_comp_barcodes : Bool, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 If provided, the barcode sequence reads will be reverse complemented
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 prior to demultiplexing.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 rev_comp_mapping_barcodes : Bool, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 If provided, the barcode sequences in the sample metadata will be
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 reverse complemented prior to demultiplexing.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
82 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84 The resulting demultiplexed sequences.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 error_correction_details : ErrorCorrectionDetails
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 Detail about the barcode error corrections.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
90 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
91 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
92 </tool>