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comparison qiime2/qiime_cutadapt_demux-single.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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-1:000000000000 0:370e0b6e9826
1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single" version="2019.4">
3 <description> - Demultiplex single-end sequence data with barcodes in- sequence.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime cutadapt demux-single
9
10 --i-seqs=$iseqs
11 --m-barcodes-column="$mbarcodescolumn"
12 --o-per-sample-sequences=opersamplesequences
13 --o-untrimmed-sequences=ountrimmedsequences
14
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 + ',' + d['additional_input'].__getattr__('file_name')
19 #end for
20 #return $file_list
21 #end def
22
23 --m-barcodes-file=$list_dict_to_string("$input_files_mbarcodesfile")
24
25 #if $perrorrate:
26 --p-error-rate=$perrorrate
27 #end if
28
29 ;
30
31 cp opersamplesequences.qza $opersamplesequences;
32 cp ountrimmedsequences.qza $ountrimmedsequences
33 ]]></command>
34 <inputs>
35 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
36 <repeat name="$input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
37 <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" />
38 </repeat>
39 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
40 <param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) 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" min="0" max="1" exclude_max="False" value="0.1"/>
41 </inputs>
42 <outputs>
43 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
44 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/>
45 </outputs>
46 <help><![CDATA[
47 Demultiplex single-end sequence data with barcodes in-sequence.
48 ###############################################################
49
50 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
51 are expected to be located within the sequence data (versus the header, or
52 a separate barcode file).
53
54 Parameters
55 ----------
56 seqs : MultiplexedSingleEndBarcodeInSequence
57 The single-end sequences to be demultiplexed.
58 barcodes : MetadataColumn[Categorical]
59 The sample metadata column listing the per-sample barcodes.
60 error_rate : Float % Range(0, 1, inclusive_end=True), optional
61 The level of error tolerance, specified as the maximum allowable error
62 rate. The default value specified by cutadapt is 0.1 (=10%), which is
63 greater than `demux emp-*`, which is 0.0 (=0%).
64
65 Returns
66 -------
67 per_sample_sequences : SampleData[SequencesWithQuality]
68 The resulting demultiplexed sequences.
69 untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence
70 The sequences that were unmatched to barcodes.
71 ]]></help>
72 <macros>
73 <import>qiime_citation.xml</import>
74 </macros>
75 <expand macro="qiime_citation"/>
76 </tool>