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comparison qiime2/qiime_cutadapt_demux-paired.xml @ 4:914fa4daf16a draft

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Fixes
author florianbegusch
date Wed, 31 Jul 2019 03:06:00 -0400
parents 51025741f326
children f190567fe3f6
comparison
equal deleted inserted replaced
3:558645416841 4:914fa4daf16a
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 #def list_dict_to_string(list_dict): 12 #if $input_files_mforwardbarcodesfile:
13 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name') 13 #def list_dict_to_string_forward(list_dict):
14 #for d in list_dict[1:]: 14 #set $file_list = list_dict[0]['additional_input'].__getattr__('file_name')
15 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name') 15 #for d in list_dict[1:]:
16 #end for 16 #set $file_list = $file_list + ',' + d['additional_input'].__getattr__('file_name')
17 #return $file_list 17 #end for
18 #return $file_list
18 #end def 19 #end def
19 20 --m-forward-barcodes-file=$list_dict_to_string_forward($input_files_mforwardbarcodesfile)
20 #if $input_files_mforwardbarcodesfile:
21 --m-forward-barcodes-file=$list_dict_to_string("$input_files_mforwardbarcodesfile")
22 #end if 21 #end if
23 22
24 #if $input_files_mreversebarcodesfile: 23 #if $input_files_mreversebarcodesfile:
25 --m-reverse-barcodes-file=$list_dict_to_string("$input_files_mreversebarcodesfile") 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($input_files_mreversebarcodesfile)
26 #end if 32 #end if
27 33
34
35
36
37 #if '__sq__' in str($mforwardbarcodescolumn):
38 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__sq__', "'")
39 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
40 #end if
41
42 #if '__db__' in str($mforwardbarcodescolumn):
43 #set $mforwardbarcodescolumn_temp = $mforwardbarcodescolumn.replace('__db__', '"')
44 #set $mforwardbarcodescolumn = $mforwardbarcodescolumn_temp
45 #end if
46
47 #if str($mforwardbarcodescolumn):
28 --m-forward-barcodes-column="$mforwardbarcodescolumn" 48 --m-forward-barcodes-column="$mforwardbarcodescolumn"
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 = $mreversebarcodescolumn_temp
62 #end if
29 63
30 #if str($mreversebarcodescolumn): 64 #if str($mreversebarcodescolumn):
31 --m-reverse-barcodes-column="$mreversebarcodescolumn" 65 --m-reverse-barcodes-column="$mreversebarcodescolumn"
32 #end if 66 #end if
33 67
68
69
34 #if $perrorrate: 70 #if $perrorrate:
35 --p-error-rate=$perrorrate 71 --p-error-rate=$perrorrate
36 #end if 72 #end if
73
37 74
38 75
39 --o-per-sample-sequences=opersamplesequences 76 --o-per-sample-sequences=opersamplesequences
40 --o-untrimmed-sequences=ountrimmedsequences 77 --o-untrimmed-sequences=ountrimmedsequences
41 ; 78 ;