Mercurial > repos > florianbegusch > qiime2_wrappers

comparison qiime2/qiime_cutadapt_trim-single.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
11 #set $pcores = '${GALAXY_SLOTS:-4}' 11 #set $pcores = '${GALAXY_SLOTS:-4}'
12 #if str($pcores): 12 #if str($pcores):
13 --p-cores=$pcores 13 --p-cores=$pcores
14 #end if 14 #end if
15 15
16
17 #if '__sq__' in str($padapter):
18 #set $padapter_temp = $padapter.replace('__sq__', "'")
19 #set $padapter = $padapter_temp
20 #end if
21
22 #if 'X' in str($padapter):
23 #set $padapter_temp = $padapter.replace('X', "$")
24 #set $padapter = $padapter_temp
25 #end if
26
16 #if str($padapter): 27 #if str($padapter):
17 --p-adapter="$padapter" 28 --p-adapter="$padapter"
29 #end if
30
31
32
33
34
35 #if '__sq__' in str($pfront):
36 #set $pfront_temp = $pfront.replace('__sq__', "'")
37 #set $pfront = $pfront_temp
18 #end if 38 #end if
19 39
20 #if str($pfront): 40 #if str($pfront):
21 --p-front="$pfront" 41 --p-front="$pfront"
22 #end if 42 #end if
43
44
45
46
23 47
24 #if '__sq__' in str($panywhere): 48 #if '__sq__' in str($panywhere):
25 #set $panywhere_temp = $panywhere.replace('__sq__', "'") 49 #set $panywhere_temp = $panywhere.replace('__sq__', "'")
26 #set $panywhere = $panywhere_temp 50 #set $panywhere = $panywhere_temp
27 #end if 51 #end if
29 #if str($panywhere): 53 #if str($panywhere):
30 --p-anywhere="$panywhere" 54 --p-anywhere="$panywhere"
31 #end if 55 #end if
32 56
33 57
34 #if $perrorrate: 58
59
60 #if str($perrorrate):
35 --p-error-rate=$perrorrate 61 --p-error-rate=$perrorrate
36 #end if 62 #end if
37 63
38 #if $pnoindels: 64 #if $pnoindels:
39 --p-no-indels 65 --p-no-indels
40 #end if 66 #end if
41 67
42 #if $ptimes: 68 #if str($ptimes):
43 --p-times=$ptimes 69 --p-times=$ptimes
44 #end if 70 #end if
45 71
46 #if $poverlap: 72 #if str($poverlap):
47 --p-overlap=$poverlap 73 --p-overlap=$poverlap
48 #end if 74 #end if
49 75
50 #if $pmatchreadwildcards: 76 #if $pmatchreadwildcards:
51 --p-match-read-wildcards 77 --p-match-read-wildcards
53 79
54 #if $pnomatchadapterwildcards: 80 #if $pnomatchadapterwildcards:
55 --p-no-match-adapter-wildcards 81 --p-no-match-adapter-wildcards
56 #end if 82 #end if
57 83
58 #if $pminimumlength: 84 #if str($pminimumlength):
59 --p-minimum-length=$pminimumlength 85 --p-minimum-length=$pminimumlength
60 #end if 86 #end if
61 87
62 #if $pdiscarduntrimmed: 88 #if $pdiscarduntrimmed:
63 --p-discard-untrimmed 89 --p-discard-untrimmed