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comparison qiime_dada2_denoise-single.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-single" name="qiime dada2 denoise-single" version="2018.4">
3 <description> - Denoise and dereplicate single-end sequences</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime dada2 denoise-single --i-demultiplexed-seqs=$idemultiplexedseqs --p-trunc-len="$ptrunclen"
9
10 #if $pmaxee:
11 --p-max-ee=$pmaxee
12 #end if
13
14 --o-table=otable
15
16 #if $phashedfeatureids:
17 --p-hashed-feature-ids
18 #end if
19
20 #if $ptrimleft:
21 --p-trim-left=$ptrimleft
22 #end if
23
24 #if str($pchimeramethod) != 'None':
25 --p-chimera-method=$pchimeramethod
26 #end if
27
28 #set $pnthreads = '${GALAXY_SLOTS:-4}'
29
30 #if str($pnthreads):
31 --p-n-threads="$pnthreads"
32 #end if
33
34
35 #if $pnreadslearn:
36 --p-n-reads-learn=$pnreadslearn
37 #end if
38
39 --o-representative-sequences=orepresentativesequences
40
41 #if str($cmdconfig) != 'None':
42 --cmd-config=$cmdconfig
43 #end if
44
45 #if $ptruncq:
46 --p-trunc-q=$ptruncq
47 #end if
48
49 #if $pminfoldparentoverabundance:
50 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
51 #end if
52
53 --o-denoising-stats=odenoisingstats
54 ;
55
56 cp otable.qza $otable;
57 cp orepresentativesequences.qza $orepresentativesequences;
58 cp odenoisingstats.qza $odenoisingstats;
59 ]]></command>
60 <inputs>
61 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: SampleData[PairedEndSequencesWithQuality | SequencesWithQuality] The single-end demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data"/>
62 <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="text"/>
63 <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"/>
64 <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"/>
65 <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"/>
66 <param label="--p-chimera-method: " name="pchimeramethod" optional="True" type="select">
67 <option selected="True" value="None">Selection is Optional</option>
68 <option value="pooled">pooled</option>
69 <option value="consensus">consensus</option>
70 <option value="none">none</option>
71 </param>
72 <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"/>
73 <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"/>
74 <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"/>
75 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
76 </inputs>
77 <outputs>
78 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
79 <data format="qza" label="${tool.name} on ${on_string}: representative-sequences.qza" name="orepresentativesequences"/>
80 <data format="qza" label="${tool.name} on ${on_string}: denoising-stats.qza" name="odenoisingstats"/>
81 </outputs>
82 <help><![CDATA[
83 Denoise and dereplicate single-end sequences
84 --------------------------------------------
85
86 This method denoises single-end sequences, dereplicates them, and filters
87 chimeras.
88
89 Parameters
90 ----------
91 demultiplexed_seqs : SampleData[PairedEndSequencesWithQuality | SequencesWithQuality]
92 The single-end demultiplexed sequences 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 chimera_method : Str % Choices({'consensus', 'none', 'pooled'}), optional
111 The method used to remove chimeras. "none": No chimera removal is
112 performed. "pooled": All reads are pooled prior to chimera detection.
113 "consensus": Chimeras are detected in samples individually, and
114 sequences found chimeric in a sufficient fraction of samples are
115 removed.
116 min_fold_parent_over_abundance : Float, optional
117 The minimum abundance of potential parents of a sequence being tested
118 as chimeric, expressed as a fold-change versus the abundance of the
119 sequence being tested. Values should be greater than or equal to 1
120 (i.e. parents should be more abundant than the sequence being tested).
121 This parameter has no effect if chimera_method is "none".
122 n_reads_learn : Int, optional
123 The number of reads to use when training the error model. Smaller
124 numbers will result in a shorter run time but a less reliable error
125 model.
126 hashed_feature_ids : Bool, optional
127 If true, the feature ids in the resulting table will be presented as
128 hashes of the sequences defining each feature. The hash will always be
129 the same for the same sequence so this allows feature tables to be
130 merged across runs of this method. You should only merge tables if the
131 exact same parameters are used for each run.
132
133 Returns
134 -------
135 table : FeatureTable[Frequency]
136 The resulting feature table.
137 representative_sequences : FeatureData[Sequence]
138 The resulting feature sequences. Each feature in the feature table will
139 be represented by exactly one sequence.
140 ]]>
141 </help>
142 </tool>