Mercurial > repos > florianbegusch > qiime2_wrappers

comparison qiime2/qiime_cutadapt_trim-paired.xml @ 4:71f124e02000 draft default tip

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:40:25 -0400
parents 149432539226
children
comparison
equal deleted inserted replaced
3:eda5df31da55 4:71f124e02000
12 #set $pcores = '${GALAXY_SLOTS:-4}' 12 #set $pcores = '${GALAXY_SLOTS:-4}'
13 #if str($pcores): 13 #if str($pcores):
14 --p-cores=$pcores 14 --p-cores=$pcores
15 #end if 15 #end if
16 16
17
18
19 #if '__sq__' in str($padapterf):
20 #set $padapterf_temp = $padapterf.replace('__sq__', "'")
21 #set $padapterf = $padapterf_temp
22 #end if
23
24 #if 'X' in str($padapterf):
25 #set $padapterf_temp = $padapterf.replace('X', "$")
26 #set $padapterf = $padapterf_temp
27 #end if
28
17 #if str($padapterf): 29 #if str($padapterf):
18 --p-adapter-f="$padapterf" 30 --p-adapter-f="$padapterf"
19 #end if 31 #end if
20 32
33
34
35
36 #if '__sq__' in str($pfrontf):
37 #set $pfrontf_temp = $pfrontf.replace('__sq__', "'")
38 #set $pfrontf = $pfrontf_temp
39 #end if
40
21 #if str($pfrontf): 41 #if str($pfrontf):
22 --p-front-f="$pfrontf" 42 --p-front-f="$pfrontf"
23 #end if 43 #end if
44
45
46
24 47
25 #if '__sq__' in str($panywheref): 48 #if '__sq__' in str($panywheref):
26 #set $panywheref_temp = $panywheref.replace('__sq__', "'") 49 #set $panywheref_temp = $panywheref.replace('__sq__', "'")
27 #set $panywheref = $panywheref_temp 50 #set $panywheref = $panywheref_temp
28 #end if 51 #end if
30 #if str($panywheref): 53 #if str($panywheref):
31 --p-anywhere-f="$panywheref" 54 --p-anywhere-f="$panywheref"
32 #end if 55 #end if
33 56
34 57
58
59
60
61 #if '__sq__' in str($padapterr):
62 #set $padapterr_temp = $padapterr.replace('__sq__', "'")
63 #set $padapterr = $padapterr_temp
64 #end if
65
66 #if 'X' in str($padapterr):
67 #set $padapterr_temp = $padapterr.replace('X', "$")
68 #set $padapterr = $padapterr_temp
69 #end if
70
35 #if str($padapterr): 71 #if str($padapterr):
36 --p-adapter-r="$padapterr" 72 --p-adapter-r="$padapterr"
37 #end if 73 #end if
38 74
75
76
77 #if '__sq__' in str($pfrontr):
78 #set $pfrontr_temp = $pfrontr.replace('__sq__', "'")
79 #set $pfrontr = $pfrontr_temp
80 #end if
81
39 #if str($pfrontr): 82 #if str($pfrontr):
40 --p-front-r="$pfrontr" 83 --p-front-r="$pfrontr"
41 #end if 84 #end if
85
86
42 87
43 #if '__sq__' in str($panywherer): 88 #if '__sq__' in str($panywherer):
44 #set $panywherer_temp = $panywherer.replace('__sq__', "'") 89 #set $panywherer_temp = $panywherer.replace('__sq__', "'")
45 #set $panywherer = $panywherer_temp 90 #set $panywherer = $panywherer_temp
46 #end if 91 #end if
47 92
48 #if str($panywherer): 93 #if str($panywherer):
49 --p-anywhere-r="$panywherer" 94 --p-anywhere-r="$panywherer"
50 #end if 95 #end if
51 96
52 #if $perrorrate: 97
98
99 #if str($perrorrate):
53 --p-error-rate=$perrorrate 100 --p-error-rate=$perrorrate
54 #end if 101 #end if
55 102
56 #if $pnoindels: 103 #if $pnoindels:
57 --p-no-indels 104 --p-no-indels
59 106
60 #if $ptimes: 107 #if $ptimes:
61 --p-times=$ptimes 108 --p-times=$ptimes
62 #end if 109 #end if
63 110
64 #if $poverlap: 111 #if str($poverlap):
65 --p-overlap=$poverlap 112 --p-overlap=$poverlap
66 #end if 113 #end if
67 114
68 #if $pmatchreadwildcards: 115 #if $pmatchreadwildcards:
69 --p-match-read-wildcards 116 --p-match-read-wildcards