Mercurial > repos > florianbegusch > qiime2_suite
comparison qiime2/qiime_dada2_denoise-single.xml @ 6:de4c22a52df4 draft
Fixes
author | florianbegusch |
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date | Tue, 13 Aug 2019 07:46:48 -0400 |
parents | 914fa4daf16a |
children | f190567fe3f6 |
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5:a025a4a89e07 | 6:de4c22a52df4 |
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6 </requirements> | 6 </requirements> |
7 <command><![CDATA[ | 7 <command><![CDATA[ |
8 qiime dada2 denoise-single | 8 qiime dada2 denoise-single |
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 str($pchimeramethod) != 'None': | 28 #if str($pchimeramethod) != 'None': |
26 --p-chimera-method=$pchimeramethod | 29 --p-chimera-method=$pchimeramethod |
27 #end if | 30 #end if |
28 | 31 |
29 #if $pminfoldparentoverabundance: | 32 #if str($pminfoldparentoverabundance): |
30 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance | 33 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance |
31 #end if | 34 #end if |
32 | 35 |
33 #set $pnthreads = '${GALAXY_SLOTS:-4}' | 36 #set $pnthreads = '${GALAXY_SLOTS:-4}' |
34 #if str($pnthreads): | 37 #if str($pnthreads): |
35 --p-n-threads="$pnthreads" | 38 --p-n-threads="$pnthreads" |
36 #end if | 39 #end if |
37 | 40 |
38 | 41 |
39 #if $pnreadslearn: | 42 #if str($pnreadslearn): |
40 --p-n-reads-learn=$pnreadslearn | 43 --p-n-reads-learn=$pnreadslearn |
41 #end if | 44 #end if |
42 | 45 |
43 #if $pnohashedfeatureids: | 46 #if str($pnohashedfeatureids): |
44 --p-no-hashed-feature-ids | 47 --p-no-hashed-feature-ids |
45 #end if | 48 #end if |
46 | 49 |
47 --o-table=otable | 50 --o-table=otable |
48 --o-representative-sequences=orepresentativesequences | 51 --o-representative-sequences=orepresentativesequences |