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

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author florianbegusch
date Wed, 14 Aug 2019 15:12:48 -0400
parents 914fa4daf16a
children a0a8d77a991c
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8:d66c7509e8f9 9:f190567fe3f6
1 <?xml version="1.0" ?> 1 <?xml version="1.0" ?>
2 <tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired" version="2019.4"> 2 <tool id="qiime_cutadapt_demux-paired" name="qiime cutadapt demux-paired" version="2019.7">
3 <description> - Demultiplex paired-end sequence data with barcodes in- sequence.</description> 3 <description> - Demultiplex paired-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-paired 8 qiime cutadapt demux-paired
9 --i-seqs=$iseqs 9 --i-seqs=$iseqs
10 10
11 11
12 #if $input_files_mforwardbarcodesfile: 12 #if $input_files_mforwardbarcodesfile:
13 #def list_dict_to_string_forward(list_dict): 13 #def list_dict_to_string_forward(list_dict):
14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 #for d in list_dict[1:]: 15 #for d in list_dict[1:]:
16 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 16 #set $file_list = $file_list + ' --m-forward-barcodes-file=' + d['additional_input'].__getattr__('file_name')
17 #end for 17 #end for
18 #return $file_list 18 #return $file_list
19 #end def 19 #end def
20 --m-forward-barcodes-file=$list_dict_to_string_forward($input_files_mforwardbarcodesfile) 20 --m-forward-barcodes-file=$list_dict_to_string_forward($input_files_mforwardbarcodesfile)
21 #end if 21 #end if
22 22
23 #if $input_files_mreversebarcodesfile: 23 #if $input_files_mreversebarcodesfile:
24 #def list_dict_to_string_reverse(list_dict): 24 #def list_dict_to_string_reverse(list_dict):
25 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 25 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
26 #for d in list_dict[1:]: 26 #for d in list_dict[1:]:
27 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 27 #set $file_list = $file_list + ' --m-reverse-barcodes-file=' + d['additional_input'].__getattr__('file_name')
28 #end for 28 #end for
29 #return $file_list 29 #return $file_list
30 #end def 30 #end def
31 --m-reverse-barcodes-file=$list_dict_to_string_reverse($input_files_mreversebarcodesfile) 31 --m-reverse-barcodes-file=$list_dict_to_string_reverse($input_files_mreversebarcodesfile)
32 #end if
33
34
35
36 #if str($pbatchsize):
37 --p-batch-size $pbatchsize
38 #end if
39
40 #if str($pminimumlength):
41 --p-minimum-length $pminimumlength
32 #end if 42 #end if
33 43
34 44
35 45
36 46
42 #if '__db__' in str($mforwardbarcodescolumn): 52 #if '__db__' in str($mforwardbarcodescolumn):
43 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__db__', '"') 53 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__db__', '"')
44 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp 54 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
45 #end if 55 #end if
46 56
47 #if str($mforwardbarcodescolumn):
48 --m-forward-barcodes-column="$mforwardbarcodescolumn"
49 #end if
50
51 57
52 58
53 59
54 #if '__sq__' in str($mreversebarcodescolumn): 60 #if '__sq__' in str($mreversebarcodescolumn):
55 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__sq__', "'") 61 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__sq__', "'")
59 #if '__db__' in str($mreversebarcodescolumn): 65 #if '__db__' in str($mreversebarcodescolumn):
60 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__db__', '"') 66 #set $mreversebarcodescolumn_temp = $mreversebarcodescolumn.replace('__db__', '"')
61 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp 67 #set $mreversebarcodescolumn = $mreversebarcodescolumn_temp
62 #end if 68 #end if
63 69
70
71
72 #if str($mforwardbarcodescolumn):
73 --m-forward-barcodes-column="$mforwardbarcodescolumn"
74 #end if
75
64 #if str($mreversebarcodescolumn): 76 #if str($mreversebarcodescolumn):
65 --m-reverse-barcodes-column="$mreversebarcodescolumn" 77 --m-reverse-barcodes-column="$mreversebarcodescolumn"
66 #end if 78 #end if
67 79
68 80
69 81
70 #if $perrorrate: 82 #if str($perrorrate):
71 --p-error-rate=$perrorrate 83 --p-error-rate=$perrorrate
72 #end if 84 #end if
73 85
74 86
75 87
79 91
80 cp opersamplesequences.qza $opersamplesequences; 92 cp opersamplesequences.qza $opersamplesequences;
81 cp ountrimmedsequences.qza $ountrimmedsequences 93 cp ountrimmedsequences.qza $ountrimmedsequences
82 ]]></command> 94 ]]></command>
83 <inputs> 95 <inputs>
96
97 <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"/>
98 <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"/>
99
100
101
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"/> 102 <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"/> 103 <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"/> 104 <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"/>
87 105
88 <repeat name="input_files_mforwardbarcodesfile" optional="False" title="--m-forward-barcodes-file"> 106 <repeat name="input_files_mforwardbarcodesfile" optional="False" title="--m-forward-barcodes-file">
99 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/> 117 <data format="qza" label="${tool.name} on ${on_string}: persamplesequences.qza" name="opersamplesequences"/>
100 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/> 118 <data format="qza" label="${tool.name} on ${on_string}: untrimmedsequences.qza" name="ountrimmedsequences"/>
101 </outputs> 119 </outputs>
102 <help><![CDATA[ 120 <help><![CDATA[
103 Demultiplex paired-end sequence data with barcodes in-sequence. 121 Demultiplex paired-end sequence data with barcodes in-sequence.
104 ############################################################### 122 ################################################################
105 123
106 Demultiplex sequence data (i.e., map barcode reads to sample ids). Barcodes 124 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 125 are expected to be located within the sequence data (versus the header, or
108 a separate barcode file). 126 a separate barcode file).
109 127
118 The sample metadata column listing the per-sample barcodes for the 136 The sample metadata column listing the per-sample barcodes for the
119 reverse reads. 137 reverse reads.
120 error_rate : Float % Range(0, 1, inclusive_end=True), optional 138 error_rate : Float % Range(0, 1, inclusive_end=True), optional
121 The level of error tolerance, specified as the maximum allowable error 139 The level of error tolerance, specified as the maximum allowable error
122 rate. 140 rate.
141 batch_size : Int % Range(0, None), optional
142 The number of samples cutadapt demultiplexes concurrently.
143 Demultiplexing in smaller batches will yield the same result with
144 marginal speed loss, and may solve "too many files" errors related to
145 sample quantity. Set to "0" to process all samples at once.
146 minimum_length : Int % Range(1, None), optional
147 Discard reads shorter than specified value. Note, the cutadapt default
148 of 0 has been overridden, because that value produces empty sequence
149 records.
123 150
124 Returns 151 Returns
125 ------- 152 -------
126 per_sample_sequences : SampleData[PairedEndSequencesWithQuality] 153 per_sample_sequences : SampleData[PairedEndSequencesWithQuality]
127 The resulting demultiplexed sequences. 154 The resulting demultiplexed sequences.