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comparison qiime2/qiime_deblur_denoise-other.xml @ 6:de4c22a52df4 draft

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 370e0b6e9826
children f190567fe3f6
comparison
equal deleted inserted replaced
5:a025a4a89e07 6:de4c22a52df4
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime deblur denoise-other 8 qiime deblur denoise-other
9 9
10 --i-demultiplexed-seqs=$idemultiplexedseqs 10 --i-demultiplexed-seqs=$idemultiplexedseqs
11 --i-reference-seqs=$ireferenceseqs 11 --i-reference-seqs=$ireferenceseqs
12 --p-trim-length="$ptrimlength"
13 12
14 #if $plefttrimlen: 13 #if str($ptrimlength):
14 --p-trim-length="$ptrimlength"
15 #end if
16
17 #if str($plefttrimlen):
15 --p-left-trim-len=$plefttrimlen 18 --p-left-trim-len=$plefttrimlen
16 #end if 19 #end if
17 20
18 #if $psamplestats: 21 #if str($psamplestats):
19 --p-sample-stats 22 --p-sample-stats
20 #end if 23 #end if
21 24
22 #if $pmeanerror: 25 #if str($pmeanerror):
23 --p-mean-error=$pmeanerror 26 --p-mean-error=$pmeanerror
24 #end if 27 #end if
25 28
26 #if $pindelprob: 29 #if str($pindelprob):
27 --p-indel-prob=$pindelprob 30 --p-indel-prob=$pindelprob
28 #end if 31 #end if
29 32
30 #if $pindelmax: 33 #if str($pindelmax):
31 --p-indel-max=$pindelmax 34 --p-indel-max=$pindelmax
32 #end if 35 #end if
33 36
34 #if $pminreads: 37 #if str($pminreads):
35 --p-min-reads=$pminreads 38 --p-min-reads=$pminreads
36 #end if 39 #end if
37 40
38 #if $pminsize: 41 #if str($pminsize):
39 --p-min-size=$pminsize 42 --p-min-size=$pminsize
40 #end if 43 #end if
41 44
42 #set $pjobstostart = '${GALAXY_SLOTS:-4}' 45 #set $pjobstostart = '${GALAXY_SLOTS:-4}'
43 46
44 #if str($pjobstostart): 47 #if str($pjobstostart):
45 --p-jobs-to-start="$pjobstostart" 48 --p-jobs-to-start="$pjobstostart"
46 #end if 49 #end if
47 50
48 51
49 #if $pnohashedfeatureids: 52 #if str($pnohashedfeatureids):
50 --p-no-hashed-feature-ids 53 --p-no-hashed-feature-ids
51 #end if 54 #end if
52 55
53 --o-table=otable 56 --o-table=otable
54 --o-representative-sequences=orepresentativesequences 57 --o-representative-sequences=orepresentativesequences