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comparison qiime2/qiime_dada2_denoise-paired.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_dada2_denoise-paired" name="qiime dada2 denoise-paired" version="2018.4">
3 <description> - Denoise and dereplicate paired-end sequences</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime dada2 denoise-paired --i-demultiplexed-seqs=$idemultiplexedseqs --p-trunc-len-f="$ptrunclenf" --p-trunc-len-r="$ptrunclenr"
9
10 #if $pmaxee:
11 --p-max-ee=$pmaxee
12 #end if
13
14 #if $ptrimleftr:
15 --p-trim-left-r=$ptrimleftr
16 #end if
17
18 --o-table=otable
19
20 #if $phashedfeatureids:
21 --p-hashed-feature-ids
22 #else
23 --p-no-hashed-feature-ids
24 #end if
25
26 #set $pnthreads = '${GALAXY_SLOTS:-4}'
27
28 #if str($pnthreads):
29 --p-n-threads=$pnthreads
30 #end if
31
32 #if $ptrimleftf:
33 --p-trim-left-f=$ptrimleftf
34 #end if
35
36 #if str($pchimeramethod) != 'None':
37 --p-chimera-method=$pchimeramethod
38 #end if
39
40 #if $pnreadslearn:
41 --p-n-reads-learn=$pnreadslearn
42 #end if
43
44 --o-representative-sequences=orepresentativesequences
45
46 #if str($cmdconfig) != 'None':
47 --cmd-config=$cmdconfig
48 #end if
49
50 #if $ptruncq:
51 --p-trunc-q=$ptruncq
52 #end if
53
54 --o-denoising-stats=odenoisingstats
55
56 #if $pminfoldparentoverabundance:
57 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
58 #end if
59 ;
60 cp otable.qza $otable;
61 cp odenoisingstats.qza $odenoisingstats;
62 cp orepresentativesequences.qza $orepresentativesequences;
63 ]]></command>
64 <inputs>
65 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: SampleData[PairedEndSequencesWithQuality] The paired-end demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
66 <param label="--p-trunc-len-f: 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" type="integer" value="0"/>
67 <param label="--p-trunc-len-r: 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" type="integer" value="0"/>
68 <param label="--p-trim-left-f: 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"/>
69 <param label="--p-trim-left-r: 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"/>
70 <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"/>
71 <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_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"/>
72 <param label="--p-chimera-method: The method used to remove chimeras. None:
73 No chimera removal is performed. Pooled:
74 All reads are pooled prior to chimera
75 detection. Consensus: Chimeras are
76 detected in samples individually, and
77 sequences found chimeric in a sufficient
78 fraction of samples are removed. [default:
79 consensus]" name="pchimeramethod" optional="True" type="select">
80 <option selected="True" value="None">Selection is Optional</option>
81 <option value="pooled">pooled</option>
82 <option value="consensus">consensus</option>
83 <option value="none">none</option>
84 </param>
85 <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"/>
86 <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"/>
87 <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="False" type="boolean"/>
88 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
89 </inputs>
90 <outputs>
91 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
92 <data format="qza" label="${tool.name} on ${on_string}: representative-sequences.qza" name="orepresentativesequences"/>
93 <data format="qza" label="${tool.name} on ${on_string}: denoising-stats.qza" name="odenoisingstats"/>
94 </outputs>
95
96 <help><![CDATA[
97 Denoise and dereplicate paired-end sequences
98 --------------------------------------------
99
100 This method denoises paired-end sequences, dereplicates them, and filters
101 chimeras.
102
103 Parameters
104 ----------
105 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality]
106 The paired-end demultiplexed sequences to be denoised.
107 trunc_len_f : Int
108 Position at which forward read sequences should be truncated due to
109 decrease in quality. This truncates the 3' end of the of the input
110 sequences, which will be the bases that were sequenced in the last
111 cycles. Reads that are shorter than this value will be discarded. After
112 this parameter is applied there must still be at least a 20 nucleotide
113 overlap between the forward and reverse reads. If 0 is provided, no
114 truncation or length filtering will be performed
115 trunc_len_r : Int
116 Position at which reverse read sequences should be truncated due to
117 decrease in quality. This truncates the 3' end of the of the input
118 sequences, which will be the bases that were sequenced in the last
119 cycles. Reads that are shorter than this value will be discarded. After
120 this parameter is applied there must still be at least a 20 nucleotide
121 overlap between the forward and reverse reads. If 0 is provided, no
122 truncation or length filtering will be performed
123 trim_left_f : Int, optional
124 Position at which forward read sequences should be trimmed due to low
125 quality. This trims the 5' end of the input sequences, which will be
126 the bases that were sequenced in the first cycles.
127 trim_left_r : Int, optional
128 Position at which reverse read sequences should be trimmed due to low
129 quality. This trims the 5' end of the input sequences, which will be
130 the bases that were sequenced in the first cycles.
131 max_ee : Float, optional
132 Reads with number of expected errors higher than this value will be
133 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 chimera_method : Str % Choices({'consensus', 'none', 'pooled'}), optional
140 The method used to remove chimeras. "none": No chimera removal is
141 performed. "pooled": All reads are pooled prior to chimera detection.
142 "consensus": Chimeras are detected in samples individually, and
143 sequences found chimeric in a sufficient fraction of samples are
144 removed.
145 min_fold_parent_over_abundance : Float, optional
146 The minimum abundance of potential parents of a sequence being tested
147 as chimeric, expressed as a fold-change versus the abundance of the
148 sequence being tested. Values should be greater than or equal to 1
149 (i.e. parents should be more abundant than the sequence being tested).
150 This parameter has no effect if chimera_method is "none".
151 n_reads_learn : Int, optional
152 The number of reads to use when training the error model. Smaller
153 numbers will result in a shorter run time but a less reliable error
154 model.
155 hashed_feature_ids : Bool, optional
156 If true, the feature ids in the resulting table will be presented as
157 hashes of the sequences defining each feature. The hash will always be
158 the same for the same sequence so this allows feature tables to be
159 merged across runs of this method. You should only merge tables if the
160 exact same parameters are used for each run.
161
162 Returns
163 -------
164 table : FeatureTable[Frequency]
165 The resulting feature table.
166 representative_sequences : FeatureData[Sequence]
167 The resulting feature sequences. Each feature in the feature table will
168 be represented by exactly one sequence, and these sequences will be the
169 joined paired-end sequences.
170 ]]>
171 </help>
172 <macros>
173 <import>qiime_citation.xml</import>
174 </macros>
175 <expand macro="qiime_citation" />
176 </tool>