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comparison qiime2/qiime_dada2_denoise-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
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3:eda5df31da55 4:71f124e02000
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
64 <option value="pooled">pooled</option> 67 <option value="pooled">pooled</option>
65 <option value="none">none</option> 68 <option value="none">none</option>
66 </param> 69 </param>
67 <param label="--p-min-fold-parent-over-abundance: NUMBER The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is 'none'. [default: 1.0]" name="pminfoldparentoverabundance" optional="True" type="float" value="1.0"/> 70 <param label="--p-min-fold-parent-over-abundance: NUMBER The minimum abundance of potential parents of a sequence being tested as chimeric, expressed as a fold-change versus the abundance of the sequence being tested. Values should be greater than or equal to 1 (i.e. parents should be more abundant than the sequence being tested). This parameter has no effect if chimera-method is 'none'. [default: 1.0]" name="pminfoldparentoverabundance" optional="True" type="float" value="1.0"/>
68 <param label="--p-n-reads-learn: INTEGER The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model. [default: 1000000]" name="pnreadslearn" optional="True" type="integer" value="1000000"/> 71 <param label="--p-n-reads-learn: INTEGER The number of reads to use when training the error model. Smaller numbers will result in a shorter run time but a less reliable error model. [default: 1000000]" name="pnreadslearn" optional="True" type="integer" value="1000000"/>
69 <param label="--p-no-hashed-feature-ids: If false, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: Fales]" name="pnohashedfeatureids" selected="False" type="boolean"/> 72 <param label="--p-no-hashed-feature-ids: If false, the feature ids in the resulting table will be presented as hashes of the sequences defining each feature. The hash will always be the same for the same sequence so this allows feature tables to be merged across runs of this method. You should only merge tables if the exact same parameters are used for each run. [default: False]" name="pnohashedfeatureids" selected="False" type="boolean"/>
70 </inputs> 73 </inputs>
71 <outputs> 74 <outputs>
72 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/> 75 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
73 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/> 76 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/>
74 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats"/> 77 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats"/>