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comparison qiime2/qiime_deblur_denoise-other.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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28:c28331a63dfd 29:3ba9833030c1
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>