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comparison qiime2-2020.8/qiime_deblur_denoise-16S.xml @ 0:5c352d975ef7 draft

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author florianbegusch
date Thu, 03 Sep 2020 09:33:04 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_deblur_denoise-16S" name="qiime deblur denoise-16S"
3 version="2020.8">
4 <description>Deblur sequences using a 16S positive filter.</description>
5 <requirements>
6 <requirement type="package" version="2020.8">qiime2</requirement>
7 </requirements>
8 <command><![CDATA[
9 qiime deblur denoise-16S
10
11 --i-demultiplexed-seqs=$idemultiplexedseqs
12
13 --p-trim-length=$ptrimlength
14
15 --p-left-trim-len=$plefttrimlen
16
17 #if $psamplestats:
18 --p-sample-stats
19 #end if
20
21 --p-mean-error=$pmeanerror
22
23 --p-indel-prob=$pindelprob
24
25 --p-indel-max=$pindelmax
26
27 --p-min-reads=$pminreads
28
29 --p-min-size=$pminsize
30
31 --p-jobs-to-start=$pjobstostart
32
33 #if $pnohashedfeatureids:
34 --p-no-hashed-feature-ids
35 #end if
36
37 --o-table=otable
38
39 --o-representative-sequences=orepresentativesequences
40
41 --o-stats=ostats
42
43 #if str($examples) != 'None':
44 --examples=$examples
45 #end if
46
47 ;
48 cp ostats.qza $ostats
49
50 ]]></command>
51 <inputs>
52 <param format="qza,no_unzip.zip" label="--i-demultiplexed-seqs: ARTIFACT SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality] The demultiplexed sequences to be denoised. [required]" name="idemultiplexedseqs" optional="False" type="data" />
53 <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" type="text" />
54 <param label="--p-left-trim-len: INTEGER Range(0, None) Sequence trimming from the 5\' end. A value of 0 will disable this trim. [default: 0]" min="0" name="plefttrimlen" optional="True" type="integer" value="0" />
55 <param label="--p-sample-stats: --p-sample-stats: / --p-no-sample-stats If true, gather stats per sample. [default: False]" name="psamplestats" selected="False" type="boolean" />
56 <param label="--p-mean-error: NUMBER The mean per nucleotide error, used for original sequence estimate. [default: 0.005]" name="pmeanerror" optional="True" type="float" value="0.005" />
57 <param label="--p-indel-prob: NUMBER Insertion/deletion (indel) probability (same for N indels). [default: 0.01]" name="pindelprob" optional="True" type="float" value="0.01" />
58 <param label="--p-indel-max: INTEGER Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3" />
59 <param label="--p-min-reads: INTEGER Retain only features appearing at least min-reads times across all samples in the resulting feature table. [default: 10]" name="pminreads" optional="True" type="integer" value="10" />
60 <param label="--p-min-size: INTEGER In each sample, discard all features with an abundance less than min-size. [default: 2]" name="pminsize" optional="True" type="integer" value="2" />
61 <param label="--p-no-hashed-feature-ids: Do not if true, hash the feature IDs. [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
62 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
63
64 </inputs>
65
66 <outputs>
67 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
68 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
69 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
70
71 </outputs>
72
73 <help><![CDATA[
74 Deblur sequences using a 16S positive filter.
75 ###############################################################
76
77 Perform sequence quality control for Illumina data using the Deblur
78 workflow with a 16S reference as a positive filter. Only forward reads are
79 supported at this time. The specific reference used is the 88% OTUs from
80 Greengenes 13_8. This mode of operation should only be used when data were
81 generated from a 16S amplicon protocol on an Illumina platform. The
82 reference is only used to assess whether each sequence is likely to be 16S
83 by a local alignment using SortMeRNA with a permissive e-value; the
84 reference is not used to characterize the sequences.
85
86 Parameters
87 ----------
88 demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
89 The demultiplexed sequences to be denoised.
90 trim_length : Int
91 Sequence trim length, specify -1 to disable trimming.
92 left_trim_len : Int % Range(0, None), optional
93 Sequence trimming from the 5' end. A value of 0 will disable this trim.
94 sample_stats : Bool, optional
95 If true, gather stats per sample.
96 mean_error : Float, optional
97 The mean per nucleotide error, used for original sequence estimate.
98 indel_prob : Float, optional
99 Insertion/deletion (indel) probability (same for N indels).
100 indel_max : Int, optional
101 Maximum number of insertion/deletions.
102 min_reads : Int, optional
103 Retain only features appearing at least min_reads times across all
104 samples in the resulting feature table.
105 min_size : Int, optional
106 In each sample, discard all features with an abundance less than
107 min_size.
108 jobs_to_start : Int, optional
109 Number of jobs to start (if to run in parallel).
110 hashed_feature_ids : Bool, optional
111 If true, hash the feature IDs.
112
113 Returns
114 -------
115 table : FeatureTable[Frequency]
116 The resulting denoised feature table.
117 representative_sequences : FeatureData[Sequence]
118 The resulting feature sequences.
119 stats : DeblurStats
120 Per-sample stats if requested.
121 ]]></help>
122 <macros>
123 <import>qiime_citation.xml</import>
124 </macros>
125 <expand macro="qiime_citation"/>
126 </tool>