|
0
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_dada2_denoise-single" name="qiime dada2 denoise-single" version="2018.4">
|
|
|
3 <description> - Denoise and dereplicate single-end sequences</description>
|
|
|
4 <requirements>
|
|
|
5 <requirement type="package" version="2018.4">qiime2</requirement>
|
|
|
6 </requirements>
|
|
|
7 <command><![CDATA[
|
|
|
8 qiime dada2 denoise-single --i-demultiplexed-seqs=$idemultiplexedseqs --p-trunc-len="$ptrunclen"
|
|
|
9
|
|
|
10 #if $pmaxee:
|
|
|
11 --p-max-ee=$pmaxee
|
|
|
12 #end if
|
|
|
13
|
|
|
14 --o-table=otable
|
|
|
15
|
|
|
16 #if $phashedfeatureids:
|
|
|
17 --p-hashed-feature-ids
|
|
|
18 #end if
|
|
|
19
|
|
|
20 #if $ptrimleft:
|
|
|
21 --p-trim-left=$ptrimleft
|
|
|
22 #end if
|
|
|
23
|
|
|
24 #if str($pchimeramethod) != 'None':
|
|
|
25 --p-chimera-method=$pchimeramethod
|
|
|
26 #end if
|
|
|
27
|
|
|
28 #set $pnthreads = '${GALAXY_SLOTS:-4}'
|
|
|
29
|
|
|
30 #if str($pnthreads):
|
|
|
31 --p-n-threads="$pnthreads"
|
|
|
32 #end if
|
|
|
33
|
|
|
34
|
|
|
35 #if $pnreadslearn:
|
|
|
36 --p-n-reads-learn=$pnreadslearn
|
|
|
37 #end if
|
|
|
38
|
|
|
39 --o-representative-sequences=orepresentativesequences
|
|
|
40
|
|
|
41 #if str($cmdconfig) != 'None':
|
|
|
42 --cmd-config=$cmdconfig
|
|
|
43 #end if
|
|
|
44
|
|
|
45 #if $ptruncq:
|
|
|
46 --p-trunc-q=$ptruncq
|
|
|
47 #end if
|
|
|
48
|
|
|
49 #if $pminfoldparentoverabundance:
|
|
|
50 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
|
|
|
51 #end if
|
|
|
52
|
|
|
53 --o-denoising-stats=odenoisingstats
|
|
|
54 ;
|
|
|
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: SampleData[PairedEndSequencesWithQuality | SequencesWithQuality] The single-end demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
|
|
|
62 <param label="--p-trunc-len: 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 provided, no truncation or length filtering will be performed [required]" name="ptrunclen" optional="False" type="text"/>
|
|
|
63 <param label="--p-trim-left: 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"/>
|
|
|
64 <param label="--p-max-ee: 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"/>
|
|
|
65 <param label="--p-trunc-q: 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"/>
|
|
|
66 <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
|
|
|
67 <option selected="True" value="None">Selection is Optional</option>
|
|
|
68 <option value="pooled">pooled</option>
|
|
|
69 <option value="consensus">consensus</option>
|
|
|
70 <option value="none">none</option>
|
|
|
71 </param>
|
|
|
72 <param label="--p-min-fold-parent-over-abundance: 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"/>
|
|
|
73 <param label="--p-hashed-feature-ids: --p-no-hashed-feature-ids 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="phashedfeatureids" checked="True" type="boolean"/>
|
|
|
74 <param label="--p-n-reads-learn: 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"/>
|
|
|
75 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
|
|
|
76 </inputs>
|
|
|
77 <outputs>
|
|
|
78 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
|
|
|
79 <data format="qza" label="${tool.name} on ${on_string}: representative-sequences.qza" name="orepresentativesequences"/>
|
|
|
80 <data format="qza" label="${tool.name} on ${on_string}: denoising-stats.qza" name="odenoisingstats"/>
|
|
|
81 </outputs>
|
|
|
82 <help><![CDATA[
|
|
|
83 Denoise and dereplicate single-end sequences
|
|
|
84 --------------------------------------------
|
|
|
85
|
|
|
86 This method denoises single-end sequences, dereplicates them, and filters
|
|
|
87 chimeras.
|
|
|
88
|
|
|
89 Parameters
|
|
|
90 ----------
|
|
|
91 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality | SequencesWithQuality]
|
|
|
92 The single-end demultiplexed sequences to be denoised.
|
|
|
93 trunc_len : Int
|
|
|
94 Position at which sequences should be truncated due to decrease in
|
|
|
95 quality. This truncates the 3' end of the of the input sequences, which
|
|
|
96 will be the bases that were sequenced in the last cycles. Reads that
|
|
|
97 are shorter than this value will be discarded. If 0 is provided, no
|
|
|
98 truncation or length filtering will be performed
|
|
|
99 trim_left : Int, optional
|
|
|
100 Position at which sequences should be trimmed due to low quality. This
|
|
|
101 trims the 5' end of the of the input sequences, which will be the bases
|
|
|
102 that were sequenced in the first cycles.
|
|
|
103 max_ee : Float, optional
|
|
|
104 Reads with number of expected errors higher than this value will be
|
|
|
105 discarded.
|
|
|
106 trunc_q : Int, optional
|
|
|
107 Reads are truncated at the first instance of a quality score less than
|
|
|
108 or equal to this value. If the resulting read is then shorter than
|
|
|
109 \`trunc_len`, it is discarded.
|
|
|
110 chimera_method : Str % Choices({'consensus', 'none', 'pooled'}), optional
|
|
|
111 The method used to remove chimeras. "none": No chimera removal is
|
|
|
112 performed. "pooled": All reads are pooled prior to chimera detection.
|
|
|
113 "consensus": Chimeras are detected in samples individually, and
|
|
|
114 sequences found chimeric in a sufficient fraction of samples are
|
|
|
115 removed.
|
|
|
116 min_fold_parent_over_abundance : Float, optional
|
|
|
117 The minimum abundance of potential parents of a sequence being tested
|
|
|
118 as chimeric, expressed as a fold-change versus the abundance of the
|
|
|
119 sequence being tested. Values should be greater than or equal to 1
|
|
|
120 (i.e. parents should be more abundant than the sequence being tested).
|
|
|
121 This parameter has no effect if chimera_method is "none".
|
|
|
122 n_reads_learn : Int, optional
|
|
|
123 The number of reads to use when training the error model. Smaller
|
|
|
124 numbers will result in a shorter run time but a less reliable error
|
|
|
125 model.
|
|
|
126 hashed_feature_ids : Bool, optional
|
|
|
127 If true, the feature ids in the resulting table will be presented as
|
|
|
128 hashes of the sequences defining each feature. The hash will always be
|
|
|
129 the same for the same sequence so this allows feature tables to be
|
|
|
130 merged across runs of this method. You should only merge tables if the
|
|
|
131 exact same parameters are used for each run.
|
|
|
132
|
|
|
133 Returns
|
|
|
134 -------
|
|
|
135 table : FeatureTable[Frequency]
|
|
|
136 The resulting feature table.
|
|
|
137 representative_sequences : FeatureData[Sequence]
|
|
|
138 The resulting feature sequences. Each feature in the feature table will
|
|
|
139 be represented by exactly one sequence.
|
|
|
140 ]]>
|
|
|
141 </help>
|
|
|
142 </tool>
|
