0
|
1 <?xml version="1.0" ?>
|
|
2 <tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired" version="2019.4">
|
|
3 <description> - Demultiplex paired-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-paired
|
|
9 --i-seqs=$iseqs
|
|
10
|
2
|
11
|
4
|
12 #if $input_files_mforwardbarcodesfile:
|
|
13 #def list_dict_to_string_forward(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 + ',' + d['additional_input'].__getattr__('file_name')
|
|
17 #end for
|
|
18 #return $file_list
|
0
|
19 #end def
|
4
|
20 --m-forward-barcodes-file=$list_dict_to_string_forward($input_files_mforwardbarcodesfile)
|
2
|
21 #end if
|
|
22
|
|
23 #if $input_files_mreversebarcodesfile:
|
4
|
24 #def list_dict_to_string_reverse(list_dict):
|
|
25 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
|
|
26 #for d in list_dict[1:]:
|
|
27 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
|
|
28 #end for
|
|
29 #return $file_list
|
|
30 #end def
|
|
31 --m-reverse-barcodes-file=$list_dict_to_string_reverse($input_files_mreversebarcodesfile)
|
|
32 #end if
|
|
33
|
|
34
|
|
35
|
|
36
|
|
37 #if '__sq__' in str($mforwardbarcodescolumn):
|
|
38 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__sq__', "'")
|
|
39 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
|
2
|
40 #end if
|
0
|
41
|
4
|
42 #if '__db__' in str($mforwardbarcodescolumn):
|
|
43 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__db__', '"')
|
|
44 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
|
|
45 #end if
|
|
46
|
|
47 #if str($mforwardbarcodescolumn):
|
0
|
48 --m-forward-barcodes-column="$mforwardbarcodescolumn"
|
4
|
49 #end if
|
|
50
|
|
51
|
|
52
|
|
53
|
|
54 #if '__sq__' in str($mreversebarcodescolumn):
|
|
55 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__sq__', "'")
|
|
56 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
|
|
57 #end if
|
|
58
|
|
59 #if '__db__' in str($mreversebarcodescolumn):
|
|
60 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__db__', '"')
|
|
61 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
|
|
62 #end if
|
0
|
63
|
|
64 #if str($mreversebarcodescolumn):
|
|
65 --m-reverse-barcodes-column="$mreversebarcodescolumn"
|
|
66 #end if
|
|
67
|
4
|
68
|
|
69
|
0
|
70 #if $perrorrate:
|
|
71 --p-error-rate=$perrorrate
|
|
72 #end if
|
|
73
|
|
74
|
4
|
75
|
0
|
76 --o-per-sample-sequences=opersamplesequences
|
|
77 --o-untrimmed-sequences=ountrimmedsequences
|
|
78 ;
|
|
79
|
|
80 cp opersamplesequences.qza $opersamplesequences;
|
|
81 cp ountrimmedsequences.qza $ountrimmedsequences
|
|
82 ]]></command>
|
|
83 <inputs>
|
|
84 <param format="qza,no_unzip.zip" label="--i-seqs: ARTIFACT MultiplexedPairedEndBarcodeInSequence The paired-end sequences to be demultiplexed. [required]" name="iseqs" optional="False" type="data"/>
|
|
85 <param label="--m-forward-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the forward reads. [required]" name="mforwardbarcodescolumn" optional="False" type="text"/>
|
|
86 <param label="--m-reverse-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes for the reverse reads. [optional]" name="mreversebarcodescolumn" optional="True" type="text"/>
|
|
87
|
|
88 <repeat name="input_files_mforwardbarcodesfile" optional="False" title="--m-forward-barcodes-file">
|
|
89 <param label="--m-forward-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
90 </repeat>
|
|
91
|
|
92 <repeat name="input_files_mreversebarcodesfile" optional="False" title="--m-reverse-barcodes-file">
|
|
93 <param label="--m-reverse-barcodes-file: Metadata file or artifact viewable as metadata. This option may be supplied multiple times to merge metadata. [required]" name="additional_input" type="data" format="tabular,qza,no_unzip.zip" />
|
|
94 </repeat>
|
|
95
|
|
96 <param label="--p-error-rate: PROPORTION Range(0, 1, inclusive_end=True) The level of error tolerance, specified as the maximum allowable error rate. [default: 0.1]" name="perrorrate" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.1"/>
|
|
97 </inputs>
|
|
98 <outputs>
|
|
99 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
|
|
100 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/>
|
|
101 </outputs>
|
|
102 <help><![CDATA[
|
|
103 Demultiplex paired-end sequence data with barcodes in-sequence.
|
|
104 ###############################################################
|
|
105
|
|
106 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes
|
|
107 are expected to be located within the sequence data (versus the header, or
|
|
108 a separate barcode file).
|
|
109
|
|
110 Parameters
|
|
111 ----------
|
|
112 seqs : MultiplexedPairedEndBarcodeInSequence
|
|
113 The paired-end sequences to be demultiplexed.
|
|
114 forward_barcodes : MetadataColumn[Categorical]
|
|
115 The sample metadata column listing the per-sample barcodes for the
|
|
116 forward reads.
|
|
117 reverse_barcodes : MetadataColumn[Categorical], optional
|
|
118 The sample metadata column listing the per-sample barcodes for the
|
|
119 reverse reads.
|
|
120 error_rate : Float % Range(0, 1, inclusive_end=True), optional
|
|
121 The level of error tolerance, specified as the maximum allowable error
|
|
122 rate.
|
|
123
|
|
124 Returns
|
|
125 -------
|
|
126 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
|
|
127 The resulting demultiplexed sequences.
|
|
128 untrimmed_sequences : MultiplexedPairedEndBarcodeInSequence
|
|
129 The sequences that were unmatched to barcodes.
|
|
130 ]]></help>
|
|
131 <macros>
|
|
132 <import>qiime_citation.xml</import>
|
|
133 </macros>
|
|
134 <expand macro="qiime_citation"/>
|
|
135 </tool>
|