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comparison qiime2-2020.8/qiime_dada2_denoise-paired.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_dada2_denoise-paired" name="qiime dada2 denoise-paired"
3 version="2020.8">
4 <description>Denoise and dereplicate paired-end sequences</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime dada2 denoise-paired
10
11 --i-demultiplexed-seqs=$idemultiplexedseqs
12
13 --p-trunc-len-f=$ptrunclenf
14
15 --p-trunc-len-r=$ptrunclenr
16
17 --p-trim-left-f=$ptrimleftf
18
19 --p-trim-left-r=$ptrimleftr
20
21 --p-max-ee-f=$pmaxeef
22
23 --p-max-ee-r=$pmaxeer
24
25 --p-trunc-q=$ptruncq
26
27 #if str($ppoolingmethod) != 'None':
28 --p-pooling-method=$ppoolingmethod
29 #end if
30
31 #if str($pchimeramethod) != 'None':
32 --p-chimera-method=$pchimeramethod
33 #end if
34
35 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
36
37 --p-n-threads=$pnthreads
38
39 --p-n-reads-learn=$pnreadslearn
40
41 #if $pnohashedfeatureids:
42 --p-no-hashed-feature-ids
43 #end if
44
45 --o-table=otable
46
47 --o-representative-sequences=orepresentativesequences
48
49 --o-denoising-stats=odenoisingstats
50
51 #if str($examples) != 'None':
52 --examples=$examples
53 #end if
54
55 ;
56 cp odenoisingstats.qza $odenoisingstats
57
58 ]]></command>
59 <inputs>
60 <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" />
61 <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 12 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" type="text" />
62 <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 12 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" type="text" />
63 <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" />
64 <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" />
65 <param label="--p-max-ee-f: NUMBER Forward reads with number of expected errors higher than this value will be discarded. [default: 2.0]" name="pmaxeef" optional="True" type="float" value="2.0" />
66 <param label="--p-max-ee-r: NUMBER Reverse reads with number of expected errors higher than this value will be discarded. [default: 2.0]" name="pmaxeer" 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-pooling-method: " name="ppoolingmethod" optional="True" type="select">
69 <option selected="True" value="None">Selection is Optional</option>
70 <option value="independent">independent</option>
71 <option value="pseudo">pseudo</option>
72 </param>
73 <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
74 <option selected="True" value="None">Selection is Optional</option>
75 <option value="none">none</option>
76 <option value="consensus">consensus</option>
77 <option value="pooled">pooled</option>
78 </param>
79 <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" />
80 <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" />
81 <param label="--p-no-hashed-feature-ids: Do not if true, 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: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
82 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
83
84 </inputs>
85
86 <outputs>
87 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
88 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
89 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats" />
90
91 </outputs>
92
93 <help><![CDATA[
94 Denoise and dereplicate paired-end sequences
95 ###############################################################
96
97 This method denoises paired-end sequences, dereplicates them, and filters
98 chimeras.
99
100 Parameters
101 ----------
102 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
103 The paired-end demultiplexed sequences to be denoised.
104 trunc_len_f : Int
105 Position at which forward read sequences should be truncated due to
106 decrease in quality. This truncates the 3' end of the of the input
107 sequences, which will be the bases that were sequenced in the last
108 cycles. Reads that are shorter than this value will be discarded. After
109 this parameter is applied there must still be at least a 12 nucleotide
110 overlap between the forward and reverse reads. If 0 is provided, no
111 truncation or length filtering will be performed
112 trunc_len_r : Int
113 Position at which reverse read sequences should be truncated due to
114 decrease in quality. This truncates the 3' end of the of the input
115 sequences, which will be the bases that were sequenced in the last
116 cycles. Reads that are shorter than this value will be discarded. After
117 this parameter is applied there must still be at least a 12 nucleotide
118 overlap between the forward and reverse reads. If 0 is provided, no
119 truncation or length filtering will be performed
120 trim_left_f : Int, optional
121 Position at which forward read sequences should be trimmed due to low
122 quality. This trims the 5' end of the input sequences, which will be
123 the bases that were sequenced in the first cycles.
124 trim_left_r : Int, optional
125 Position at which reverse read sequences should be trimmed due to low
126 quality. This trims the 5' end of the input sequences, which will be
127 the bases that were sequenced in the first cycles.
128 max_ee_f : Float, optional
129 Forward reads with number of expected errors higher than this value
130 will be discarded.
131 max_ee_r : Float, optional
132 Reverse reads with number of expected errors higher than this value
133 will be discarded.
134 trunc_q : Int, optional
135 Reads are truncated at the first instance of a quality score less than
136 or equal to this value. If the resulting read is then shorter than
137 `trunc_len_f` or `trunc_len_r` (depending on the direction of the read)
138 it is discarded.
139 pooling_method : Str % Choices('independent', 'pseudo'), optional
140 The method used to pool samples for denoising. "independent": Samples
141 are denoised indpendently. "pseudo": The pseudo-pooling method is used
142 to approximate pooling of samples. In short, samples are denoised
143 independently once, ASVs detected in at least 2 samples are recorded,
144 and samples are denoised independently a second time, but this time
145 with prior knowledge of the recorded ASVs and thus higher sensitivity
146 to those ASVs.
147 chimera_method : Str % Choices('consensus', 'none', 'pooled'), optional
148 The method used to remove chimeras. "none": No chimera removal is
149 performed. "pooled": All reads are pooled prior to chimera detection.
150 "consensus": Chimeras are detected in samples individually, and
151 sequences found chimeric in a sufficient fraction of samples are
152 removed.
153 min_fold_parent_over_abundance : Float, optional
154 The minimum abundance of potential parents of a sequence being tested
155 as chimeric, expressed as a fold-change versus the abundance of the
156 sequence being tested. Values should be greater than or equal to 1
157 (i.e. parents should be more abundant than the sequence being tested).
158 This parameter has no effect if chimera_method is "none".
159 n_threads : Int, optional
160 The number of threads to use for multithreaded processing. If 0 is
161 provided, all available cores will be used.
162 n_reads_learn : Int, optional
163 The number of reads to use when training the error model. Smaller
164 numbers will result in a shorter run time but a less reliable error
165 model.
166 hashed_feature_ids : Bool, optional
167 If true, the feature ids in the resulting table will be presented as
168 hashes of the sequences defining each feature. The hash will always be
169 the same for the same sequence so this allows feature tables to be
170 merged across runs of this method. You should only merge tables if the
171 exact same parameters are used for each run.
172
173 Returns
174 -------
175 table : FeatureTable[Frequency]
176 The resulting feature table.
177 representative_sequences : FeatureData[Sequence]
178 The resulting feature sequences. Each feature in the feature table will
179 be represented by exactly one sequence, and these sequences will be the
180 joined paired-end sequences.
181 denoising_stats : SampleData[DADA2Stats]
182 ]]></help>
183 <macros>
184 <import>qiime_citation.xml</import>
185 </macros>
186 <expand macro="qiime_citation"/>
187 </tool>