Mercurial > repos > florianbegusch > qiime2_all

comparison qiime_demux_emp-single.xml @ 0:09b7bcb72fa7 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:09b7bcb72fa7
1 <?xml version="1.0" ?>
2 <tool id="qiime_demux_emp-single" name="qiime demux emp-single" version="2018.4">
3 <description>- Demultiplex 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-single --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 $opersamplesequences;
37 ]]></command>
38 <inputs>
39 <param format="qza,no_unzip.zip" label="--i-seqs: EMPPairedEndSequences | EMPSingleEndSequences | RawSequences The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
40 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
41 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip"/>
42 </repeat>
43 <param label="--m-barcodes-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. The sample metadata column containing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
44 <param label="--p-rev-comp-barcodes: --p-no-rev-comp-barcodes If provided, the barcode sequence reads will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompbarcodes" checked="False" type="boolean"/>
45 <param label="--p-rev-comp-mapping-barcodes: --p-no-rev-comp-mapping-barcodes If provided, the barcode sequences in the sample metadata will be reverse complemented prior to demultiplexing. [default: False]" name="prevcompmappingbarcodes" checked="False" type="boolean"/>
46 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
47 </inputs>
48 <outputs>
49 <data format="qza" label="${tool.name} on ${on_string}: per-sample-sequences.qza" name="opersamplesequences"/>
50 </outputs>
51 <help><![CDATA[
52 Demultiplex sequence data generated with the EMP protocol.
53 ----------------------------------------------------------
54
55 Demultiplex sequence data (i.e., map barcode reads to sample ids) for data
56 generated with the Earth Microbiome Project (EMP) amplicon sequencing
57 protocol. Details about this protocol can be found at
58 http://www.earthmicrobiome.org/protocols-and-standards/
59
60 Parameters
61 ----------
62 seqs : EMPPairedEndSequences | EMPSingleEndSequences | RawSequences
63 The single-end sequences to be demultiplexed.
64 barcodes : MetadataColumn[Categorical]
65 The sample metadata column containing the per-sample barcodes.
66 rev_comp_barcodes : Bool, optional
67 If provided, the barcode sequence reads will be reverse complemented
68 prior to demultiplexing.
69 rev_comp_mapping_barcodes : Bool, optional
70 If provided, the barcode sequences in the sample metadata will be
71 reverse complemented prior to demultiplexing.
72
73 Returns
74 -------
75 per_sample_sequences : SampleData[SequencesWithQuality]
76 The resulting demultiplexed sequences.
77 ]]>
78 </help>
79 </tool>