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comparison qiime_dada2_denoise-pyro.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_dada2_denoise-pyro" name="qiime dada2 denoise-pyro" version="2018.4">
3 <description> - Denoise and dereplicate single-end pyrosequences</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8
9 qiime dada2 denoise-pyro --p-trunc-len="$ptrunclen" --i-demultiplexed-seqs=$idemultiplexedseqs
10
11 #if $pnreadslearn:
12 --p-n-reads-learn=$pnreadslearn
13 #end if
14
15 #if str($pchimeramethod) != 'None':
16 --p-chimera-method=$pchimeramethod
17 #end if
18
19 --o-representative-sequences=orepresentativesequences
20
21 #if $pminfoldparentoverabundance:
22 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
23 #end if
24
25 #if str($cmdconfig) != 'None':
26 --cmd-config=$cmdconfig
27 #end if
28
29 #if $pmaxlen:
30 --p-max-len=$pmaxlen
31 #end if
32
33 --o-table=otable
34
35 #if $ptruncq:
36 --p-trunc-q=$ptruncq
37 #end if
38
39 #set $pnthreads = '${GALAXY_SLOTS:-4}'
40
41 #if str($pnthreads):
42 --p-n-threads="$pnthreads"
43 #end if
44
45
46 #if $ptrimleft:
47 --p-trim-left=$ptrimleft
48 #end if
49
50 #if $phashedfeatureids:
51 --p-hashed-feature-ids
52 #end if
53
54 #if $pmaxee:
55 --p-max-ee=$pmaxee
56 #end if
57
58 --o-denoising-stats=odenoisingstats;
59
60 cp orepresentativesequences.qza $orepresentativesequences;
61 cp otable.qza $otable;
62 cp odenoisingstats.qza $odenoisingstats;
63 ]]></command>
64 <inputs>
65 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: SampleData[SequencesWithQuality] The single-end demultiplexed pyrosequencing sequences (e.g. 454, IonTorrent) to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
66
67 <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="integer" value="0"/>
68 <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"/>
69 <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"/>
70
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`, it is discarded. [default: 2]" name="ptruncq" optional="True" type="integer" value="2"/>
72
73 <param label="--p-max-len: 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"/>
74
75 <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
76 <option selected="True" value="None">Selection is Optional</option>
77 <option value="consensus">consensus</option>
78 <option value="none">none</option>
79 <option value="pooled">pooled</option>
80 </param>
81
82 <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"/>
83
84 <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: 250000]" name="pnreadslearn" optional="True" type="integer" value="250000"/>
85
86 <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"/>
87
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 ${on_string}: representative-sequences.qza" name="orepresentativesequences"/>
92 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
93 <data format="qza" label="${tool.name} on ${on_string}: denoising-stats.qza" name="odenoisingstats"/>
94 </outputs>
95 <help>
96 <![CDATA[
97 Denoise and dereplicate single-end pyrosequences
98 -------------------------------------------------
99 This method denoises single-end pyrosequencing sequences, dereplicates
100 them, and filters chimeras.
101
102 Parameters
103 ----------
104 demultiplexed_seqs : SampleData[SequencesWithQuality]
105 The single-end demultiplexed pyrosequencing sequences (e.g. 454,
106 IonTorrent) to be denoised.
107 trunc_len : Int
108 Position at which sequences should be truncated due to decrease in
109 quality. This truncates the 3' end of the of the input sequences, which
110 will be the bases that were sequenced in the last cycles. Reads that
111 are shorter than this value will be discarded. If 0 is provided, no
112 truncation or length filtering will be performed
113 trim_left : Int, optional
114 Position at which sequences should be trimmed due to low quality. This
115 trims the 5' end of the of the input sequences, which will be the bases
116 that were sequenced in the first cycles.
117 max_ee : Float, optional
118 Reads with number of expected errors higher than this value will be
119 discarded.
120 trunc_q : Int, optional
121 Reads are truncated at the first instance of a quality score less than
122 or equal to this value. If the resulting read is then shorter than
123 `trunc_len`, it is discarded.
124 max_len : Int, optional
125 Remove reads prior to trimming or truncation which are longer than this
126 value. If 0 is provided no reads will be removed based on length.
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 \
162 ]]>
163 </help>
164 </tool>