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comparison qiime2/qiime_cutadapt_demux-single.xml @ 9:f190567fe3f6 draft

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author florianbegusch
date Wed, 14 Aug 2019 15:12:48 -0400
parents 914fa4daf16a
children a0a8d77a991c
comparison
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8:d66c7509e8f9 9:f190567fe3f6
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single" version="2019.4"> 2 <tool id="qiime_cutadapt_demux-single" name="qiime cutadapt demux-single" version="2019.7">
3 <description> - Demultiplex single-end sequence data with barcodes in- sequence.</description> 3 <description> - Demultiplex single-end sequence data with barcodes in- sequence.</description>
4 <requirements> 4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement> 5 <requirement type="package" version="2019.7">qiime2</requirement>
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime cutadapt demux-single 8 qiime cutadapt demux-single
9 9
10 --i-seqs=$iseqs 10 --i-seqs=$iseqs
11
12
13 #if str($pbatchsize):
14 --p-batch-size $pbatchsize
15 #end if
16
17 #if str($pminimumlength):
18 --p-minimum-length $pminimumlength
19 #end if
20
21
22
23
24
25 #if $input_files_mbarcodesfile:
26 #def list_dict_to_string(list_dict):
27 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
28 #for d in list_dict[1:]:
29 #set $file_list = $file_list + ' --m-barcodes-file=' + d['additional_input'].__getattr__('file_name')
30 #end for
31 #return $file_list
32 #end def
33 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
34 #end if
11 35
12 36
13 37
14 #if '__sq__' in str($mbarcodescolumn): 38 #if '__sq__' in str($mbarcodescolumn):
15 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'") 39 #set $mbarcodescolumn_temp = $mbarcodescolumn.replace('__sq__', "'")
17 #end if 41 #end if
18 42
19 --m-barcodes-column="$mbarcodescolumn" 43 --m-barcodes-column="$mbarcodescolumn"
20 44
21 45
22 --o-per-sample-sequences=opersamplesequences
23 --o-untrimmed-sequences=ountrimmedsequences
24 46
25 47 #if str($perrorrate):
26 48 --p-error-rate=$perrorrate
27
28
29
30 #if $input_files_mbarcodesfile:
31 #def list_dict_to_string(list_dict):
32 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
33 #for d in list_dict[1:]:
34 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
35 #end for
36 #return $file_list
37 #end def
38 --m-barcodes-file=$list_dict_to_string($input_files_mbarcodesfile)
39 #end if 49 #end if
40 50
41 51
42 #if $perrorrate: 52 --o-per-sample-sequences=opersamplesequences
43 --p-error-rate=$perrorrate 53 --o-untrimmed-sequences=ountrimmedsequences
44 #end if
45
46 ; 54 ;
47 55
48 cp opersamplesequences.qza $opersamplesequences; 56 cp opersamplesequences.qza $opersamplesequences;
49 cp ountrimmedsequences.qza $ountrimmedsequences 57 cp ountrimmedsequences.qza $ountrimmedsequences
50 ]]></command> 58 ]]></command>
51 <inputs> 59 <inputs>
60
61 <param label="--p-batch-size: INTEGER The number of samples cutadapt demultiplexes Range(0, None) concurrently. Demultiplexing in smaller batches will yield the same result with marginal speed loss, and may solve 'too many files' errors related to sample quantity. Set to '0' to process all samples at once. [default: 0]" name="pbatchsize" optional="True" type="integer" value="0" min="0"/>
62 <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]" name="pminimumlength" optional="True" type="integer" value="1" min="1"/>
63
64
52 <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 <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"/>
53 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file"> 66 <repeat name="input_files_mbarcodesfile" optional="False" title="--m-barcodes-file">
54 <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" /> 67 <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" />
55 </repeat> 68 </repeat>
56 <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 label="--m-barcodes-column: COLUMN MetadataColumn[Categorical] The sample metadata column listing the per-sample barcodes. [required]" name="mbarcodescolumn" optional="False" type="text"/>
76 The sample metadata column listing the per-sample barcodes. 89 The sample metadata column listing the per-sample barcodes.
77 error_rate : Float % Range(0, 1, inclusive_end=True), optional 90 error_rate : Float % Range(0, 1, inclusive_end=True), optional
78 The level of error tolerance, specified as the maximum allowable error 91 The level of error tolerance, specified as the maximum allowable error
79 rate. The default value specified by cutadapt is 0.1 (=10%), which is 92 rate. The default value specified by cutadapt is 0.1 (=10%), which is
80 greater than `demux emp-*`, which is 0.0 (=0%). 93 greater than `demux emp-*`, which is 0.0 (=0%).
94 batch_size : Int % Range(0, None), optional
95 The number of samples cutadapt demultiplexes concurrently.
96 Demultiplexing in smaller batches will yield the same result with
97 marginal speed loss, and may solve "too many files" errors related to
98 sample quantity. Set to "0" to process all samples at once.
99 minimum_length : Int % Range(1, None), optional
100 Discard reads shorter than specified value. Note, the cutadapt default
101 of 0 has been overridden, because that value produces empty sequence
102 records.
81 103
82 Returns 104 Returns
83 ------- 105 -------
84 per_sample_sequences : SampleData[SequencesWithQuality] 106 per_sample_sequences : SampleData[SequencesWithQuality]
85 The resulting demultiplexed sequences. 107 The resulting demultiplexed sequences.