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comparison qiime2/qiime_dada2_denoise-pyro.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
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
139 The resulting feature table. 142 The resulting feature table.
140 representative_sequences : FeatureData[Sequence] 143 representative_sequences : FeatureData[Sequence]
141 The resulting feature sequences. Each feature in the feature table will 144 The resulting feature sequences. Each feature in the feature table will
142 be represented by exactly one sequence. 145 be represented by exactly one sequence.
143 denoising_stats : SampleData[DADA2Stats] 146 denoising_stats : SampleData[DADA2Stats]
147 \
144 ]]></help> 148 ]]></help>
145 <macros> 149 <macros>
146 <import>qiime_citation.xml</import> 150 <import>qiime_citation.xml</import>
147 </macros> 151 </macros>
148 <expand macro="qiime_citation"/> 152 <expand macro="qiime_citation"/>