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comparison qiime2/qiime_cutadapt_demux-single.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_cutadapt_demux-single" name="qiime cutadapt demux-single" version="2018.4">
3 <description> - Demultiplex single-end sequence data with barcodes in- sequence.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8
9 qiime cutadapt demux-single
10
11 #def list_dict_to_string(list_dict):
12 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
13 #for d in list_dict[1:]:
14 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
15 #end for
16 #return $file_list
17 #end def
18
19 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile) --i-seqs=$iseqs --m-barcodes-column="$mbarcodescolumn"
20
21 #if str($cmdconfig) != 'None':
22 --cmd-config=$cmdconfig
23 #end if
24
25 --o-per-sample-sequences=opersamplesequences --o-untrimmed-sequences=ountrimmedsequences
26
27 #if $perrorrate:
28 --p-error-rate=$perrorrate
29 #end if
30 ;
31 cp opersamplesequences.qza $opersamplesequences;
32 cp ountrimmedsequences.qza $ountrimmedsequences;
33 ]]></command>
34 <inputs>
35 <param format="qza,no_unzip.zip" label="--i-seqs: MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
36
37 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
38 <param label="--m-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
39 </repeat>
40 <param label="--m-barcodes-column: MetadataColumn[Categorical] Column from metadata file or artifact viewable as metadata. The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
41
42 <param label="--p-error-rate: The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). [default: 0.1]" name="perrorrate" optional="True" type="float" value="0.1"/>
43
44 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
45 </inputs>
46 <outputs>
47 <data format="qza" label="${tool.name} on ${on_string}: per-sample-sequences.qza" name="opersamplesequences"/>
48 <data format="qza" label="${tool.name} on ${on_string}: untrimmed-sequences.qza" name="ountrimmedsequences"/>
49 </outputs>
50 <help><![CDATA[
51 Demultiplex single-end sequence data with barcodes in-sequence.
52 ----------------------------------------------------------------
53
54 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
55 are expected to be located within the sequence data (versus the header, or
56 a separate barcode file).
57
58 Parameters
59 ----------
60 seqs : MultiplexedSingleEndBarcodeInSequence
61 The single-end sequences to be demultiplexed.
62 barcodes : MetadataColumn[Categorical]
63 The sample metadata column listing the per-sample barcodes.
64 error_rate : Float % Range(0, 1, inclusive_end=True), optional
65 The level of error tolerance, specified as the maximum allowable error
66 rate. The default value specified by cutadapt is 0.1 (=10%), which is
67 greater than `demux emp-*`, which is 0.0 (=0%).
68
69 Returns
70 -------
71 per_sample_sequences : SampleData[SequencesWithQuality]
72 The resulting demultiplexed sequences.
73 untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence
74 The sequences that were unmatched to barcodes.
75 ]]>
76 </help>
77 <macros>
78 <import>qiime_citation.xml</import>
79 </macros>
80 <expand macro="qiime_citation" />
81 </tool>