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