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