annotate qiime2-2020.8/qiime_deblur_denoise-16S.xml @ 20:d93d8888f0b0 draft

Uploaded
author florianbegusch
date Fri, 04 Sep 2020 12:44:24 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
20
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
1 <?xml version="1.0" ?>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
2 <tool id="qiime_deblur_denoise-16S" name="qiime deblur denoise-16S"
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
3 version="2020.8">
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
4 <description>Deblur sequences using a 16S positive filter.</description>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
5 <requirements>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
6 <requirement type="package" version="2020.8">qiime2</requirement>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
7 </requirements>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
8 <command><![CDATA[
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
9 qiime deblur denoise-16S
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
10
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
11 --i-demultiplexed-seqs=$idemultiplexedseqs
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
12
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
13 --p-trim-length=$ptrimlength
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
14
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
15 --p-left-trim-len=$plefttrimlen
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
16
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
17 #if $psamplestats:
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
18 --p-sample-stats
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
19 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
20
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
21 --p-mean-error=$pmeanerror
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
22
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
23 --p-indel-prob=$pindelprob
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
24
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
25 --p-indel-max=$pindelmax
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
26
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
27 --p-min-reads=$pminreads
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
28
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
29 --p-min-size=$pminsize
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
30
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
31 --p-jobs-to-start=$pjobstostart
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
32
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
33 #if $pnohashedfeatureids:
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
34 --p-no-hashed-feature-ids
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
35 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
36
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
37 --o-table=otable
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
38
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
39 --o-representative-sequences=orepresentativesequences
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
40
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
41 --o-stats=ostats
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
42
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
43 #if str($examples) != 'None':
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
44 --examples=$examples
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
45 #end if
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
46
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
47 ;
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
48 cp ostats.qza $ostats
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
49
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
50 ]]></command>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
51 <inputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
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" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
53 <param label="--p-trim-length: INTEGER Sequence trim length, specify -1 to disable trimming. [required]" name="ptrimlength" optional="False" type="text" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
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" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
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" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
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" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
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" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
58 <param label="--p-indel-max: INTEGER Maximum number of insertion/deletions. [default: 3]" name="pindelmax" optional="True" type="integer" value="3" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
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" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
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" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
61 <param label="--p-no-hashed-feature-ids: Do not if true, hash the feature IDs. [default: True]" name="pnohashedfeatureids" selected="False" type="boolean" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
62 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
63
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
64 </inputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
65
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
66 <outputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
67 <data format="qza" label="${tool.name} on ${on_string}: table.qza" name="otable" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
68 <data format="qza" label="${tool.name} on ${on_string}: representativesequences.qza" name="orepresentativesequences" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
69 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
70
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
71 </outputs>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
72
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
73 <help><![CDATA[
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
74 Deblur sequences using a 16S positive filter.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
75 ###############################################################
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
76
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
77 Perform sequence quality control for Illumina data using the Deblur
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
78 workflow with a 16S reference as a positive filter. Only forward reads are
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
79 supported at this time. The specific reference used is the 88% OTUs from
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
80 Greengenes 13_8. This mode of operation should only be used when data were
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
81 generated from a 16S amplicon protocol on an Illumina platform. The
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
82 reference is only used to assess whether each sequence is likely to be 16S
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
83 by a local alignment using SortMeRNA with a permissive e-value; the
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
84 reference is not used to characterize the sequences.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
85
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
86 Parameters
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
87 ----------
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
88 demultiplexed_seqs : SampleData[SequencesWithQuality | PairedEndSequencesWithQuality | JoinedSequencesWithQuality]
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
89 The demultiplexed sequences to be denoised.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
90 trim_length : Int
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
91 Sequence trim length, specify -1 to disable trimming.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
92 left_trim_len : Int % Range(0, None), optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
93 Sequence trimming from the 5' end. A value of 0 will disable this trim.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
94 sample_stats : Bool, optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
95 If true, gather stats per sample.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
96 mean_error : Float, optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
97 The mean per nucleotide error, used for original sequence estimate.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
98 indel_prob : Float, optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
99 Insertion/deletion (indel) probability (same for N indels).
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
100 indel_max : Int, optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
101 Maximum number of insertion/deletions.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
102 min_reads : Int, optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
103 Retain only features appearing at least min_reads times across all
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
104 samples in the resulting feature table.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
105 min_size : Int, optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
106 In each sample, discard all features with an abundance less than
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
107 min_size.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
108 jobs_to_start : Int, optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
109 Number of jobs to start (if to run in parallel).
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
110 hashed_feature_ids : Bool, optional
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
111 If true, hash the feature IDs.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
112
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
113 Returns
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
114 -------
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
115 table : FeatureTable[Frequency]
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
116 The resulting denoised feature table.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
117 representative_sequences : FeatureData[Sequence]
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
118 The resulting feature sequences.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
119 stats : DeblurStats
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
120 Per-sample stats if requested.
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
121 ]]></help>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
122 <macros>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
123 <import>qiime_citation.xml</import>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
124 </macros>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
125 <expand macro="qiime_citation"/>
d93d8888f0b0 Uploaded
florianbegusch
parents:
diff changeset
126 </tool>