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comparison qiime2/qiime_dada2_denoise-paired.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_dada2_denoise-paired" name="qiime dada2 denoise-paired" version="2019.4">
3 <description> - Denoise and dereplicate paired-end sequences</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime dada2 denoise-paired
9
10 --i-demultiplexed-seqs=$idemultiplexedseqs
11 --p-trunc-len-f="$ptrunclenf"
12 --p-trunc-len-r="$ptrunclenr"
13 #if $ptrimleftf:
14 --p-trim-left-f=$ptrimleftf
15 #end if
16
17 #if $ptrimleftr:
18 --p-trim-left-r=$ptrimleftr
19 #end if
20
21 #if $pmaxee:
22 --p-max-ee=$pmaxee
23 #end if
24
25 #if $ptruncq:
26 --p-trunc-q=$ptruncq
27 #end if
28
29 #if str($pchimeramethod) != 'None':
30 --p-chimera-method=$pchimeramethod
31 #end if
32
33 #if $pminfoldparentoverabundance:
34 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
35 #end if
36
37 #set $pnthreads = '${GALAXY_SLOTS:-4}'
38
39 #if str($pnthreads):
40 --p-n-threads="$pnthreads"
41 #end if
42
43
44 #if $pnreadslearn:
45 --p-n-reads-learn=$pnreadslearn
46 #end if
47
48 #if $pnohashedfeatureids:
49 --p-no-hashed-feature-ids
50 #end if
51
52 --o-table=otable
53 --o-representative-sequences=orepresentativesequences
54 --o-denoising-stats=odenoisingstats
55 ;
56 cp otable.qza $otable;
57 cp orepresentativesequences.qza $orepresentativesequences;
58 cp odenoisingstats.qza $odenoisingstats
59 ]]></command>
60 <inputs>
61 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[PairedEndSequencesWithQuality] The paired-end demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
62 <param label="--p-trunc-len-f: INTEGER Position at which forward read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 20 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclenf" optional="False" value="" type="integer"/>
63 <param label="--p-trunc-len-r: INTEGER Position at which reverse read sequences should be truncated due to decrease in quality. This truncates the 3' end of the of the input sequences, which will be the bases that were sequenced in the last cycles. Reads that are shorter than this value will be discarded. After this parameter is applied there must still be at least a 20 nucleotide overlap between the forward and reverse reads. If 0 is provided, no truncation or length filtering will be performed [required]" name="ptrunclenr" optional="False" value="" type="integer"/>
64 <param label="--p-trim-left-f: INTEGER Position at which forward read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]" name="ptrimleftf" optional="True" type="integer" value="0"/>
65 <param label="--p-trim-left-r: INTEGER Position at which reverse read sequences should be trimmed due to low quality. This trims the 5' end of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]" name="ptrimleftr" optional="True" type="integer" value="0"/>
66 <param label="--p-max-ee: NUMBER Reads with number of expected errors higher than this value will be discarded. [default: 2.0]" name="pmaxee" optional="True" type="float" value="2.0"/>
67 <param label="--p-trunc-q: INTEGER Reads are truncated at the first instance of a quality score less than or equal to this value. If the resulting read is then shorter than `trunc-len-f` or `trunc-len-r` (depending on the direction of the read) it is discarded. [default: 2]" name="ptruncq" optional="True" type="integer" value="2"/>
68 <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
69 <option selected="True" value="None">Selection is Optional</option>
70 <option value="consensus">consensus</option>
71 <option value="pooled">pooled</option>
72 <option value="none">none</option>
73 </param>
74 <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"/>
75 <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"/>
76 <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"/>
77 </inputs>
78 <outputs>
79 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
80 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/>
81 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats"/>
82 </outputs>
83 <help><![CDATA[
84 Denoise and dereplicate paired-end sequences
85 ############################################
86
87 This method denoises paired-end sequences, dereplicates them, and filters
88 chimeras.
89
90 Parameters
91 ----------
92 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
93 The paired-end demultiplexed sequences to be denoised.
94 trunc_len_f : Int
95 Position at which forward read sequences should be truncated due to
96 decrease in quality. This truncates the 3' end of the of the input
97 sequences, which will be the bases that were sequenced in the last
98 cycles. Reads that are shorter than this value will be discarded. After
99 this parameter is applied there must still be at least a 20 nucleotide
100 overlap between the forward and reverse reads. If 0 is provided, no
101 truncation or length filtering will be performed
102 trunc_len_r : Int
103 Position at which reverse read sequences should be truncated due to
104 decrease in quality. This truncates the 3' end of the of the input
105 sequences, which will be the bases that were sequenced in the last
106 cycles. Reads that are shorter than this value will be discarded. After
107 this parameter is applied there must still be at least a 20 nucleotide
108 overlap between the forward and reverse reads. If 0 is provided, no
109 truncation or length filtering will be performed
110 trim_left_f : Int, optional
111 Position at which forward read sequences should be trimmed due to low
112 quality. This trims the 5' end of the input sequences, which will be
113 the bases that were sequenced in the first cycles.
114 trim_left_r : Int, optional
115 Position at which reverse read sequences should be trimmed due to low
116 quality. This trims the 5' end of the input sequences, which will be
117 the bases that were sequenced in the first cycles.
118 max_ee : Float, optional
119 Reads with number of expected errors higher than this value will be
120 discarded.
121 trunc_q : Int, optional
122 Reads are truncated at the first instance of a quality score less than
123 or equal to this value. If the resulting read is then shorter than
124 `trunc_len_f` or `trunc_len_r` (depending on the direction of the read)
125 it is discarded.
126 chimera_method : Str % Choices('consensus', 'pooled', 'none'), optional
127 The method used to remove chimeras. "none": No chimera removal is
128 performed. "pooled": All reads are pooled prior to chimera detection.
129 "consensus": Chimeras are detected in samples individually, and
130 sequences found chimeric in a sufficient fraction of samples are
131 removed.
132 min_fold_parent_over_abundance : Float, optional
133 The minimum abundance of potential parents of a sequence being tested
134 as chimeric, expressed as a fold-change versus the abundance of the
135 sequence being tested. Values should be greater than or equal to 1
136 (i.e. parents should be more abundant than the sequence being tested).
137 This parameter has no effect if chimera_method is "none".
138 provided, all available cores will be used.
139 n_reads_learn : Int, optional
140 The number of reads to use when training the error model. Smaller
141 numbers will result in a shorter run time but a less reliable error
142 model.
143 hashed_feature_ids : Bool, optional
144 If true, the feature ids in the resulting table will be presented as
145 hashes of the sequences defining each feature. The hash will always be
146 the same for the same sequence so this allows feature tables to be
147 merged across runs of this method. You should only merge tables if the
148 exact same parameters are used for each run.
149
150 Returns
151 -------
152 table : FeatureTable[Frequency]
153 The resulting feature table.
154 representative_sequences : FeatureData[Sequence]
155 The resulting feature sequences. Each feature in the feature table will
156 be represented by exactly one sequence, and these sequences will be the
157 joined paired-end sequences.
158 denoising_stats : SampleData[DADA2Stats]
159 ]]></help>
160 <macros>
161 <import>qiime_citation.xml</import>
162 </macros>
163 <expand macro="qiime_citation"/>
164 </tool>