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comparison qiime2/qiime_dada2_denoise-pyro.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-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=$idemultiplexedseqs
11 --p-trunc-len="$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 $pmaxlen:
26 --p-max-len=$pmaxlen
27 #end if
28
29 #if str($pchimeramethod) != 'None':
30 --p-chimera-method=$pchimeramethod
31 #end if
32
33 #if $pminfoldparentoverabundance:
34 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
35 #end if
36
37 #set $pnthreads = '${GALAXY_SLOTS:-4}'
38 #if str($pnthreads):
39 --p-n-threads="$pnthreads"
40 #end if
41
42
43 #if $pnreadslearn:
44 --p-n-reads-learn=$pnreadslearn
45 #end if
46
47 #if $pnohashedfeatureids:
48 --p-no-hashed-feature-ids
49 #end if
50
51 --o-table=otable
52 --o-representative-sequences=orepresentativesequences
53 --o-denoising-stats=odenoisingstats
54 ;
55 cp otable.qza $otable;
56 cp orepresentativesequences.qza $orepresentativesequences;
57 cp odenoisingstats.qza $odenoisingstats
58 ]]></command>
59 <inputs>
60 <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"/>
61 <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"/>
62 <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"/>
63 <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"/>
64 <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"/>
65 <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"/>
66 <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">
67 <option selected="True" value="None">Selection is Optional</option>
68 <option value="consensus">consensus</option>
69 <option value="pooled">pooled</option>
70 <option value="none">none</option>
71 </param>
72 <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"/>
73 <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"/>
74 <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"/>
75 </inputs>
76 <outputs>
77 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
78 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/>
79 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats"/>
80 </outputs>
81 <help><![CDATA[
82 Denoise and dereplicate single-end pyrosequences
83 ################################################
84
85 This method denoises single-end pyrosequencing sequences, dereplicates
86 them, and filters chimeras.
87
88 Parameters
89 ----------
90 demultiplexed_seqs : SampleData[SequencesWithQuality]
91 The single-end demultiplexed pyrosequencing sequences (e.g. 454,
92 IonTorrent) 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 max_len : Int, optional
111 Remove reads prior to trimming or truncation which are longer than this
112 value. If 0 is provided no reads will be removed based on length.
113 chimera_method : Str % Choices('consensus', 'pooled', 'none'), optional
114 The method used to remove chimeras. "none": No chimera removal is
115 performed. "pooled": All reads are pooled prior to chimera detection.
116 "consensus": Chimeras are detected in samples individually, and
117 sequences found chimeric in a sufficient fraction of samples are
118 removed.
119 min_fold_parent_over_abundance : Float, optional
120 The minimum abundance of potential parents of a sequence being tested
121 as chimeric, expressed as a fold-change versus the abundance of the
122 sequence being tested. Values should be greater than or equal to 1
123 (i.e. parents should be more abundant than the sequence being tested).
124 This parameter has no effect if chimera_method is "none".
125 n_reads_learn : Int, optional
126 The number of reads to use when training the error model. Smaller
127 numbers will result in a shorter run time but a less reliable error
128 model.
129 hashed_feature_ids : Bool, optional
130 If true, the feature ids in the resulting table will be presented as
131 hashes of the sequences defining each feature. The hash will always be
132 the same for the same sequence so this allows feature tables to be
133 merged across runs of this method. You should only merge tables if the
134 exact same parameters are used for each run.
135
136 Returns
137 -------
138 table : FeatureTable[Frequency]
139 The resulting feature table.
140 representative_sequences : FeatureData[Sequence]
141 The resulting feature sequences. Each feature in the feature table will
142 be represented by exactly one sequence.
143 denoising_stats : SampleData[DADA2Stats]
144 ]]></help>
145 <macros>
146 <import>qiime_citation.xml</import>
147 </macros>
148 <expand macro="qiime_citation"/>
149 </tool>