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comparison qiime2/qiime_cutadapt_demux-single.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single"
3 version="2020.8">
4 <description>Demultiplex single-end sequence data with barcodes in- sequence.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime cutadapt demux-single
10
11 --i-seqs=$iseqs
12 # if $input_files_mbarcodesfile:
13 # def list_dict_to_string(list_dict):
14 # set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 # for d in list_dict[1:]:
16 # set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name')
17 # end for
18 # return $file_list
19 # end def
20 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
21 # end if
22
23 #if '__ob__' in str($mbarcodescolumn):
24 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__ob__', '[')
25 #set $mbarcodescolumn = $mbarcodescolumn_temp
26 #end if
27 #if '__cb__' in str($mbarcodescolumn):
28 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__cb__', ']')
29 #set $mbarcodescolumn = $mbarcodescolumn_temp
30 #end if
31 #if 'X' in str($mbarcodescolumn):
32 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('X', '\\')
33 #set $mbarcodescolumn = $mbarcodescolumn_temp
34 #end if
35 #if '__sq__' in str($mbarcodescolumn):
36 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
37 #set $mbarcodescolumn = $mbarcodescolumn_temp
38 #end if
39 #if '__db__' in str($mbarcodescolumn):
40 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__db__', '"')
41 #set $mbarcodescolumn = $mbarcodescolumn_temp
42 #end if
43
44 --m-barcodes-column=$mbarcodescolumn
45
46
47 --p-error-rate=$perrorrate
48
49 --p-minimum-length=$pminimumlength
50
51 --o-per-sample-sequences=opersamplesequences
52
53 --o-untrimmed-sequences=ountrimmedsequences
54
55 #if str($examples) != 'None':
56 --examples=$examples
57 #end if
58
59 ;
60 cp ountrimmedsequences.qza $ountrimmedsequences
61
62 ]]></command>
63 <inputs>
64 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedSingleEndBarcodeInSequence The single-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data" />
65 <repeat name="input_files_mbarcodesfile" optional="True" title="--m-barcodes-file">
66 <param format="tabular,qza,no_unzip.zip" label="--m-barcodes-file: METADATA" name="additional_input" optional="True" type="data" />
67 </repeat>
68 <param label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text" />
69 <param exclude_max="False" label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. The default value specified by cutadapt is 0.1 (=10%), which is greater than `demux emp-*`, which is 0.0 (=0%). [default: 0.1]" max="1" min="0" name="perrorrate" optional="True" type="float" value="0.1" />
70 <param label="--p-minimum-length: INTEGER Range(1, None) Discard reads shorter than specified value. Note, the cutadapt default of 0 has been overridden, because that value produces empty sequence records. [default: 1]" min="1" name="pminimumlength" optional="True" type="integer" value="1" />
71 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
72
73 </inputs>
74
75 <outputs>
76 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences" />
77 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences" />
78
79 </outputs>
80
81 <help><![CDATA[
82 Demultiplex single-end sequence data with barcodes in- sequence.
83 ###############################################################
84
85 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
86 are expected to be located within the sequence data (versus the header, or
87 a separate barcode file).
88
89 Parameters
90 ----------
91 seqs : MultiplexedSingleEndBarcodeInSequence
92 The single-end sequences to be demultiplexed.
93 barcodes : MetadataColumn[Categorical]
94 The sample metadata column listing the per-sample barcodes.
95 error_rate : Float % Range(0, 1, inclusive_end=True), optional
96 The level of error tolerance, specified as the maximum allowable error
97 rate. The default value specified by cutadapt is 0.1 (=10%), which is
98 greater than `demux emp-*`, which is 0.0 (=0%).
99 batch_size : Int % Range(0, None), optional
100 The number of samples cutadapt demultiplexes concurrently.
101 Demultiplexing in smaller batches will yield the same result with
102 marginal speed loss, and may solve "too many files" errors related to
103 sample quantity. Set to "0" to process all samples at once.
104 minimum_length : Int % Range(1, None), optional
105 Discard reads shorter than specified value. Note, the cutadapt default
106 of 0 has been overridden, because that value produces empty sequence
107 records.
108
109 Returns
110 -------
111 per_sample_sequences : SampleData[SequencesWithQuality]
112 The resulting demultiplexed sequences.
113 untrimmed_sequences : MultiplexedSingleEndBarcodeInSequence
114 The sequences that were unmatched to barcodes.
115 ]]></help>
116 <macros>
117 <import>qiime_citation.xml</import>
118 </macros>
119 <expand macro="qiime_citation"/>
120 </tool>