|
2
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_dada2_denoise-pyro" name="qiime dada2 denoise-pyro" version="2019.4">
|
|
|
3 <description> - Denoise and dereplicate single-end pyrosequences</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2019.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime dada2 denoise-pyro
|
|
|
9
|
|
|
10 --i-demultiplexed-seqs=$idemultiplexedseqs
|
|
|
11
|
|
4
|
12 #if str($ptrunclen):
|
|
|
13 --p-trunc-len="$ptrunclen"
|
|
|
14 #end if
|
|
|
15
|
|
|
16 #if str($ptrimleft):
|
|
2
|
17 --p-trim-left=$ptrimleft
|
|
|
18 #end if
|
|
|
19
|
|
4
|
20 #if str($pmaxee):
|
|
2
|
21 --p-max-ee=$pmaxee
|
|
|
22 #end if
|
|
|
23
|
|
4
|
24 #if str($ptruncq):
|
|
2
|
25 --p-trunc-q=$ptruncq
|
|
|
26 #end if
|
|
|
27
|
|
4
|
28 #if str($pmaxlen):
|
|
2
|
29 --p-max-len=$pmaxlen
|
|
|
30 #end if
|
|
|
31
|
|
|
32 #if str($pchimeramethod) != 'None':
|
|
|
33 --p-chimera-method=$pchimeramethod
|
|
|
34 #end if
|
|
|
35
|
|
4
|
36 #if str($pminfoldparentoverabundance):
|
|
2
|
37 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
|
|
|
38 #end if
|
|
|
39
|
|
|
40 #set $pnthreads = '${GALAXY_SLOTS:-4}'
|
|
|
41 #if str($pnthreads):
|
|
|
42 --p-n-threads="$pnthreads"
|
|
|
43 #end if
|
|
|
44
|
|
|
45
|
|
4
|
46 #if str($pnreadslearn):
|
|
2
|
47 --p-n-reads-learn=$pnreadslearn
|
|
|
48 #end if
|
|
|
49
|
|
4
|
50 #if str($pnohashedfeatureids):
|
|
2
|
51 --p-no-hashed-feature-ids
|
|
|
52 #end if
|
|
|
53
|
|
|
54 --o-table=otable
|
|
|
55 --o-representative-sequences=orepresentativesequences
|
|
|
56 --o-denoising-stats=odenoisingstats
|
|
|
57 ;
|
|
|
58 cp otable.qza $otable;
|
|
|
59 cp orepresentativesequences.qza $orepresentativesequences;
|
|
|
60 cp odenoisingstats.qza $odenoisingstats
|
|
|
61 ]]></command>
|
|
|
62 <inputs>
|
|
|
63 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality] The single-end demultiplexed pyrosequencing sequences (e.g. 454, IonTorrent) to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
|
|
|
64 <param label="--p-trunc-len: INTEGER Position at which 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. If 0 is prov#ided, no truncation or length filtering will be performed [required]" name="ptrunclen" optional="False" value="" type="integer"/>
|
|
|
65 <param label="--p-trim-left: INTEGER Position at which sequences should be trimmed due to low quality. This trims the 5' end of the of the input sequences, which will be the bases that were sequenced in the first cycles. [default: 0]" name="ptrimleft" 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`, it is discarded. [default: 2]" name="ptruncq" optional="True" type="integer" value="2"/>
|
|
|
68 <param label="--p-max-len: INTEGER Remove reads prior to trimming or truncation which are longer than this value. If 0 is provided no reads will be removed based on length. [default: 0]" name="pmaxlen" optional="True" type="integer" value="0"/>
|
|
|
69 <param label="--p-chimera-method: The method used to remove chimeras. 'none': No chimera removal is performed. 'pooled': All reads are pooled prior to chimera detection. 'consensus': Chimeras are detected in samples individually, and sequences found chimeric in a sufficient fraction of samples are removed." name="pchimeramethod" optional="True" type="select">
|
|
|
70 <option selected="True" value="None">Selection is Optional</option>
|
|
|
71 <option value="consensus">consensus</option>
|
|
|
72 <option value="pooled">pooled</option>
|
|
|
73 <option value="none">none</option>
|
|
|
74 </param>
|
|
|
75 <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"/>
|
|
|
76 <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: 250000]" name="pnreadslearn" optional="True" type="integer" value="250000"/>
|
|
|
77 <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"/>
|
|
|
78 </inputs>
|
|
|
79 <outputs>
|
|
|
80 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
|
|
|
81 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/>
|
|
|
82 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats"/>
|
|
|
83 </outputs>
|
|
|
84 <help><![CDATA[
|
|
|
85 Denoise and dereplicate single-end pyrosequences
|
|
|
86 ################################################
|
|
|
87
|
|
|
88 This method denoises single-end pyrosequencing sequences, dereplicates
|
|
|
89 them, and filters chimeras.
|
|
|
90
|
|
|
91 Parameters
|
|
|
92 ----------
|
|
|
93 demultiplexed_seqs : SampleData[SequencesWithQuality]
|
|
|
94 The single-end demultiplexed pyrosequencing sequences (e.g. 454,
|
|
|
95 IonTorrent) to be denoised.
|
|
|
96 trunc_len : Int
|
|
|
97 Position at which sequences should be truncated due to decrease in
|
|
|
98 quality. This truncates the 3' end of the of the input sequences, which
|
|
|
99 will be the bases that were sequenced in the last cycles. Reads that
|
|
|
100 are shorter than this value will be discarded. If 0 is provided, no
|
|
|
101 truncation or length filtering will be performed
|
|
|
102 trim_left : Int, optional
|
|
|
103 Position at which sequences should be trimmed due to low quality. This
|
|
|
104 trims the 5' end of the of the input sequences, which will be the bases
|
|
|
105 that were sequenced in the first cycles.
|
|
|
106 max_ee : Float, optional
|
|
|
107 Reads with number of expected errors higher than this value will be
|
|
|
108 discarded.
|
|
|
109 trunc_q : Int, optional
|
|
|
110 Reads are truncated at the first instance of a quality score less than
|
|
|
111 or equal to this value. If the resulting read is then shorter than
|
|
|
112 `trunc_len`, it is discarded.
|
|
|
113 max_len : Int, optional
|
|
|
114 Remove reads prior to trimming or truncation which are longer than this
|
|
|
115 value. If 0 is provided no reads will be removed based on length.
|
|
|
116 chimera_method : Str % Choices('consensus', 'pooled', 'none'), optional
|
|
|
117 The method used to remove chimeras. "none": No chimera removal is
|
|
|
118 performed. "pooled": All reads are pooled prior to chimera detection.
|
|
|
119 "consensus": Chimeras are detected in samples individually, and
|
|
|
120 sequences found chimeric in a sufficient fraction of samples are
|
|
|
121 removed.
|
|
|
122 min_fold_parent_over_abundance : Float, optional
|
|
|
123 The minimum abundance of potential parents of a sequence being tested
|
|
|
124 as chimeric, expressed as a fold-change versus the abundance of the
|
|
|
125 sequence being tested. Values should be greater than or equal to 1
|
|
|
126 (i.e. parents should be more abundant than the sequence being tested).
|
|
|
127 This parameter has no effect if chimera_method is "none".
|
|
|
128 n_reads_learn : Int, optional
|
|
|
129 The number of reads to use when training the error model. Smaller
|
|
|
130 numbers will result in a shorter run time but a less reliable error
|
|
|
131 model.
|
|
|
132 hashed_feature_ids : Bool, optional
|
|
|
133 If true, the feature ids in the resulting table will be presented as
|
|
|
134 hashes of the sequences defining each feature. The hash will always be
|
|
|
135 the same for the same sequence so this allows feature tables to be
|
|
|
136 merged across runs of this method. You should only merge tables if the
|
|
|
137 exact same parameters are used for each run.
|
|
|
138
|
|
|
139 Returns
|
|
|
140 -------
|
|
|
141 table : FeatureTable[Frequency]
|
|
|
142 The resulting feature table.
|
|
|
143 representative_sequences : FeatureData[Sequence]
|
|
|
144 The resulting feature sequences. Each feature in the feature table will
|
|
|
145 be represented by exactly one sequence.
|
|
|
146 denoising_stats : SampleData[DADA2Stats]
|
|
4
|
147 \
|
|
2
|
148 ]]></help>
|
|
|
149 <macros>
|
|
|
150 <import>qiime_citation.xml</import>
|
|
|
151 </macros>
|
|
|
152 <expand macro="qiime_citation"/>
|
|
|
153 </tool>
|
