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comparison qiime2/qiime_dada2_denoise-pyro.xml @ 6:de4c22a52df4 draft

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Fixes
author florianbegusch
date Tue, 13 Aug 2019 07:46:48 -0400
parents 914fa4daf16a
children f190567fe3f6
comparison
equal deleted inserted replaced
5:a025a4a89e07 6:de4c22a52df4
6 </requirements> 6 </requirements>
7 <command><![CDATA[ 7 <command><![CDATA[
8 qiime dada2 denoise-pyro 8 qiime dada2 denoise-pyro
9 9
10 --i-demultiplexed-seqs=$idemultiplexedseqs 10 --i-demultiplexed-seqs=$idemultiplexedseqs
11 --p-trunc-len="$ptrunclen"
12 11
13 #if $ptrimleft: 12 #if str($ptrunclen):
13 --p-trunc-len="$ptrunclen"
14 #end if
15
16 #if str($ptrimleft):
14 --p-trim-left=$ptrimleft 17 --p-trim-left=$ptrimleft
15 #end if 18 #end if
16 19
17 #if $pmaxee: 20 #if str($pmaxee):
18 --p-max-ee=$pmaxee 21 --p-max-ee=$pmaxee
19 #end if 22 #end if
20 23
21 #if $ptruncq: 24 #if str($ptruncq):
22 --p-trunc-q=$ptruncq 25 --p-trunc-q=$ptruncq
23 #end if 26 #end if
24 27
25 #if $pmaxlen: 28 #if str($pmaxlen):
26 --p-max-len=$pmaxlen 29 --p-max-len=$pmaxlen
27 #end if 30 #end if
28 31
29 #if str($pchimeramethod) != 'None': 32 #if str($pchimeramethod) != 'None':
30 --p-chimera-method=$pchimeramethod 33 --p-chimera-method=$pchimeramethod
31 #end if 34 #end if
32 35
33 #if $pminfoldparentoverabundance: 36 #if str($pminfoldparentoverabundance):
34 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance 37 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
35 #end if 38 #end if
36 39
37 #set $pnthreads = '${GALAXY_SLOTS:-4}' 40 #set $pnthreads = '${GALAXY_SLOTS:-4}'
38 #if str($pnthreads): 41 #if str($pnthreads):
39 --p-n-threads="$pnthreads" 42 --p-n-threads="$pnthreads"
40 #end if 43 #end if
41 44
42 45
43 #if $pnreadslearn: 46 #if str($pnreadslearn):
44 --p-n-reads-learn=$pnreadslearn 47 --p-n-reads-learn=$pnreadslearn
45 #end if 48 #end if
46 49
47 #if $pnohashedfeatureids: 50 #if str($pnohashedfeatureids):
48 --p-no-hashed-feature-ids 51 --p-no-hashed-feature-ids
49 #end if 52 #end if
50 53
51 --o-table=otable 54 --o-table=otable
52 --o-representative-sequences=orepresentativesequences 55 --o-representative-sequences=orepresentativesequences