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comparison qiime2/qiime_demux_emp-paired.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_demux_emp-paired" name="qiime demux emp-paired" version="2018.4">
3 <description>- Demultiplex paired-end sequence data generated with the EMP protocol.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime demux emp-paired --m-barcodes-column="$mbarcodescolumn" --i-seqs=$iseqs
9
10 #def list_dict_to_string(list_dict):
11 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
12 #for d in list_dict[1:]:
13 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
14 #end for
15 #return $file_list
16 #end def
17
18 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) --o-per-sample-sequences=opersamplesequences
19
20 #if $prevcompbarcodes:
21 --p-rev-comp-barcodes
22 #else
23 --p-no-rev-comp-barcodes
24 #end if
25
26 #if $prevcompmappingbarcodes:
27 --p-rev-comp-mapping-barcodes
28 #else
29 --p-no-rev-comp-mapping-barcodes
30 #end if
31
32 #if str($cmdconfig) != 'None':
33 --cmd-config=$cmdconfig
34 #end if
35 ;
36 cp opersamplesequences.qza $opersamplesequences;
37 ]]></command>
38 <inputs>
39 <param format="qza,no_unzip.zip" label="--i-seqs: EMPPairedEndSequences The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
40 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
41 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
42 </repeat>
43 <param label="--m-barcodes-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
44 <param label="--p-rev-comp-barcodes: --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" checked="False" type="boolean"/>
45 <param label="--p-rev-comp-mapping-barcodes: --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" checked="False" type="boolean"/>
46
47 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
48 </inputs>
49 <outputs>
50 <data format="qza" label="${tool.name} on ${on_string}: per-sample-sequences.qza" name="opersamplesequences"/>
51 </outputs>
52 <help><![CDATA[
53 Demultiplex paired-end sequence data generated with the EMP protocol.
54 ---------------------------------------------------------------------
55
56 Demultiplex paired-end sequence data (i.e., map barcode reads to sample
57 ids) for data generated with the Earth Microbiome Project (EMP) amplicon
58 sequencing protocol. Details about this protocol can be found at
59 http://www.earthmicrobiome.org/protocols-and-standards/
60
61 Parameters
62 ----------
63 seqs : EMPPairedEndSequences
64 The paired-end sequences to be demultiplexed.
65 barcodes : MetadataColumn[Categorical]
66 The sample metadata column containing the per-sample barcodes.
67 rev_comp_barcodes : Bool, optional
68 If provided, the barcode sequence reads will be reverse complemented
69 prior to demultiplexing.
70 rev_comp_mapping_barcodes : Bool, optional
71 If provided, the barcode sequences in the sample metadata will be
72 reverse complemented prior to demultiplexing.
73
74 Returns
75 -------
76 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
77 The resulting demultiplexed sequences.
78 ]]>
79 </help>
80 <macros>
81 <import>qiime_citation.xml</import>
82 </macros>
83 <expand macro="qiime_citation" />
84 </tool>