annotate qiime2/qiime_dada2_denoise-pyro.xml @ 0:370e0b6e9826 draft

Uploaded
author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
parents
children 914fa4daf16a
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_dada2_denoise-pyro" name="qiime dada2 denoise-pyro" version="2019.4">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
3 <description> - Denoise and dereplicate single-end pyrosequences</description>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
4 <requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
5 <requirement type="package" version="2019.4">qiime2</requirement>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
6 </requirements>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
7 <command><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
8 qiime dada2 denoise-pyro
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
9
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
10 --i-demultiplexed-seqs=$idemultiplexedseqs
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
11 --p-trunc-len="$ptrunclen"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
12
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
13 #if $ptrimleft:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
14 --p-trim-left=$ptrimleft
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
15 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
16
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
17 #if $pmaxee:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
18 --p-max-ee=$pmaxee
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
19 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
20
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
21 #if $ptruncq:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
22 --p-trunc-q=$ptruncq
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
23 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
24
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
25 #if $pmaxlen:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
26 --p-max-len=$pmaxlen
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
27 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
28
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
29 #if str($pchimeramethod) != 'None':
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
30 --p-chimera-method=$pchimeramethod
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
31 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
32
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
33 #if $pminfoldparentoverabundance:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
34 --p-min-fold-parent-over-abundance=$pminfoldparentoverabundance
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
35 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
36
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
37 #set $pnthreads = '${GALAXY_SLOTS:-4}'
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
38 #if str($pnthreads):
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
39 --p-n-threads="$pnthreads"
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
40 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
41
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
42
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
43 #if $pnreadslearn:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
44 --p-n-reads-learn=$pnreadslearn
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
45 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
46
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
47 #if $pnohashedfeatureids:
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
48 --p-no-hashed-feature-ids
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
49 #end if
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
50
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
51 --o-table=otable
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
52 --o-representative-sequences=orepresentativesequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
53 --o-denoising-stats=odenoisingstats
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
54 ;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
55 cp otable.qza $otable;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
56 cp orepresentativesequences.qza $orepresentativesequences;
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
57 cp odenoisingstats.qza $odenoisingstats
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
58 ]]></command>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
59 <inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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">
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
67 <option selected="True" value="None">Selection is Optional</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
68 <option value="consensus">consensus</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
69 <option value="pooled">pooled</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
70 <option value="none">none</option>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
71 </param>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
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"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
75 </inputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
76 <outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
77 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
78 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
79 <data format="qza" label="${tool.name} on ${on_string}: denoisingstats.qza" name="odenoisingstats"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
80 </outputs>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
81 <help><![CDATA[
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
82 Denoise and dereplicate single-end pyrosequences
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
83 ################################################
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
84
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
85 This method denoises single-end pyrosequencing sequences, dereplicates
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
86 them, and filters chimeras.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
87
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
88 Parameters
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
89 ----------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
90 demultiplexed_seqs : SampleData[SequencesWithQuality]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
91 The single-end demultiplexed pyrosequencing sequences (e.g. 454,
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
92 IonTorrent) to be denoised.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
93 trunc_len : Int
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
94 Position at which sequences should be truncated due to decrease in
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
95 quality. This truncates the 3' end of the of the input sequences, which
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
96 will be the bases that were sequenced in the last cycles. Reads that
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
97 are shorter than this value will be discarded. If 0 is provided, no
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
98 truncation or length filtering will be performed
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
99 trim_left : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
100 Position at which sequences should be trimmed due to low quality. This
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
101 trims the 5' end of the of the input sequences, which will be the bases
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
102 that were sequenced in the first cycles.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
103 max_ee : Float, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
104 Reads with number of expected errors higher than this value will be
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
105 discarded.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
106 trunc_q : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
107 Reads are truncated at the first instance of a quality score less than
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
108 or equal to this value. If the resulting read is then shorter than
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
109 `trunc_len`, it is discarded.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
110 max_len : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
111 Remove reads prior to trimming or truncation which are longer than this
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
112 value. If 0 is provided no reads will be removed based on length.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
113 chimera_method : Str % Choices('consensus', 'pooled', 'none'), optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
114 The method used to remove chimeras. "none": No chimera removal is
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
115 performed. "pooled": All reads are pooled prior to chimera detection.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
116 "consensus": Chimeras are detected in samples individually, and
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
117 sequences found chimeric in a sufficient fraction of samples are
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
118 removed.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
119 min_fold_parent_over_abundance : Float, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
120 The minimum abundance of potential parents of a sequence being tested
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
121 as chimeric, expressed as a fold-change versus the abundance of the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
122 sequence being tested. Values should be greater than or equal to 1
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
123 (i.e. parents should be more abundant than the sequence being tested).
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
124 This parameter has no effect if chimera_method is "none".
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
125 n_reads_learn : Int, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
126 The number of reads to use when training the error model. Smaller
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
127 numbers will result in a shorter run time but a less reliable error
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
128 model.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
129 hashed_feature_ids : Bool, optional
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
130 If true, the feature ids in the resulting table will be presented as
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
131 hashes of the sequences defining each feature. The hash will always be
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
132 the same for the same sequence so this allows feature tables to be
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
133 merged across runs of this method. You should only merge tables if the
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
134 exact same parameters are used for each run.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
135
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
136 Returns
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
137 -------
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
138 table : FeatureTable[Frequency]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
139 The resulting feature table.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
140 representative_sequences : FeatureData[Sequence]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
141 The resulting feature sequences. Each feature in the feature table will
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
142 be represented by exactly one sequence.
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
143 denoising_stats : SampleData[DADA2Stats]
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
144 ]]></help>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
145 <macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
146 <import>qiime_citation.xml</import>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
147 </macros>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
148 <expand macro="qiime_citation"/>
370e0b6e9826 Uploaded
florianbegusch
parents:
diff changeset
149 </tool>