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comparison qiime2-2020.8/qiime_dada2_denoise-pyro.xml @ 20:d93d8888f0b0 draft

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author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
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19:6c48f8d82424 20:d93d8888f0b0
1 <?xml version="1.0" ?>
2 <tool id="qiime_dada2_denoise-pyro" name="qiime dada2 denoise-pyro"
3 version="2020.8">
4 <description>Denoise and dereplicate single-end pyrosequences</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime dada2 denoise-pyro
10
11 --i-demultiplexed-seqs=$idemultiplexedseqs
12
13 --p-trunc-len=$ptrunclen
14
15 --p-trim-left=$ptrimleft
16
17 --p-max-ee=$pmaxee
18
19 --p-trunc-q=$ptruncq
20
21 --p-max-len=$pmaxlen
22
23 #if str($ppoolingmethod) != 'None':
24 --p-pooling-method=$ppoolingmethod
25 #end if
26
27 #if str($pchimeramethod) != 'None':
28 --p-chimera-method=$pchimeramethod
29 #end if
30
31 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
32
33 --p-n-threads=$pnthreads
34
35 --p-n-reads-learn=$pnreadslearn
36
37 #if $pnohashedfeatureids:
38 --p-no-hashed-feature-ids
39 #end if
40
41 --o-table=otable
42
43 --o-representative-sequences=orepresentativesequences
44
45 --o-denoising-stats=odenoisingstats
46
47 #if str($examples) != 'None':
48 --examples=$examples
49 #end if
50
51 ;
52 cp odenoisingstats.qza $odenoisingstats
53
54 ]]></command>
55 <inputs>
56 <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" />
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" type="text" />
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-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" />
62 <param label="--p-pooling-method: " name="ppoolingmethod" optional="True" type="select">
63 <option selected="True" value="None">Selection is Optional</option>
64 <option value="independent">independent</option>
65 <option value="pseudo">pseudo</option>
66 </param>
67 <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
68 <option selected="True" value="None">Selection is Optional</option>
69 <option value="none">none</option>
70 <option value="consensus">consensus</option>
71 <option value="pooled">pooled</option>
72 </param>
73 <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" />
74 <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" />
75 <param label="--p-no-hashed-feature-ids: Do not 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="pnohashedfeatureids" selected="False" type="boolean" />
76 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
77
78 </inputs>
79
80 <outputs>
81 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
82 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
83 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats" />
84
85 </outputs>
86
87 <help><![CDATA[
88 Denoise and dereplicate single-end pyrosequences
89 ###############################################################
90
91 This method denoises single-end pyrosequencing sequences, dereplicates
92 them, and filters chimeras.
93
94 Parameters
95 ----------
96 demultiplexed_seqs : SampleData[SequencesWithQuality]
97 The single-end demultiplexed pyrosequencing sequences (e.g. 454,
98 IonTorrent) to be denoised.
99 trunc_len : Int
100 Position at which sequences should be truncated due to decrease in
101 quality. This truncates the 3' end of the of the input sequences, which
102 will be the bases that were sequenced in the last cycles. Reads that
103 are shorter than this value will be discarded. If 0 is provided, no
104 truncation or length filtering will be performed
105 trim_left : Int, optional
106 Position at which sequences should be trimmed due to low quality. This
107 trims the 5' end of the of the input sequences, which will be the bases
108 that were sequenced in the first cycles.
109 max_ee : Float, optional
110 Reads with number of expected errors higher than this value will be
111 discarded.
112 trunc_q : Int, optional
113 Reads are truncated at the first instance of a quality score less than
114 or equal to this value. If the resulting read is then shorter than
115 `trunc_len`, it is discarded.
116 max_len : Int, optional
117 Remove reads prior to trimming or truncation which are longer than this
118 value. If 0 is provided no reads will be removed based on length.
119 pooling_method : Str % Choices('independent', 'pseudo'), optional
120 The method used to pool samples for denoising. "independent": Samples
121 are denoised indpendently. "pseudo": The pseudo-pooling method is used
122 to approximate pooling of samples. In short, samples are denoised
123 independently once, ASVs detected in at least 2 samples are recorded,
124 and samples are denoised independently a second time, but this time
125 with prior knowledge of the recorded ASVs and thus higher sensitivity
126 to those ASVs.
127 chimera_method : Str % Choices('consensus', 'none', 'pooled'), optional
128 The method used to remove chimeras. "none": No chimera removal is
129 performed. "pooled": All reads are pooled prior to chimera detection.
130 "consensus": Chimeras are detected in samples individually, and
131 sequences found chimeric in a sufficient fraction of samples are
132 removed.
133 min_fold_parent_over_abundance : Float, optional
134 The minimum abundance of potential parents of a sequence being tested
135 as chimeric, expressed as a fold-change versus the abundance of the
136 sequence being tested. Values should be greater than or equal to 1
137 (i.e. parents should be more abundant than the sequence being tested).
138 This parameter has no effect if chimera_method is "none".
139 n_threads : Int, optional
140 The number of threads to use for multithreaded processing. If 0 is
141 provided, all available cores will be used.
142 n_reads_learn : Int, optional
143 The number of reads to use when training the error model. Smaller
144 numbers will result in a shorter run time but a less reliable error
145 model.
146 hashed_feature_ids : Bool, optional
147 If true, the feature ids in the resulting table will be presented as
148 hashes of the sequences defining each feature. The hash will always be
149 the same for the same sequence so this allows feature tables to be
150 merged across runs of this method. You should only merge tables if the
151 exact same parameters are used for each run.
152
153 Returns
154 -------
155 table : FeatureTable[Frequency]
156 The resulting feature table.
157 representative_sequences : FeatureData[Sequence]
158 The resulting feature sequences. Each feature in the feature table will
159 be represented by exactly one sequence.
160 denoising_stats : SampleData[DADA2Stats]
161 ]]></help>
162 <macros>
163 <import>qiime_citation.xml</import>
164 </macros>
165 <expand macro="qiime_citation"/>
166 </tool>