|
29
|
1 <?xml version="1.0" ?>
|
|
|
2 <tool id="qiime_vsearch_uchime-denovo" name="qiime vsearch uchime-denovo"
|
|
|
3 version="2020.8">
|
|
|
4 <description>De novo chimera filtering with vsearch.</description>
|
|
|
5 <requirements>
|
|
|
6 <requirement type="package" version="2020.8">qiime2</requirement>
|
|
|
7 </requirements>
|
|
|
8 <command><![CDATA[
|
|
|
9 qiime vsearch uchime-denovo
|
|
|
10
|
|
|
11 --i-sequences=$isequences
|
|
|
12
|
|
|
13 --i-table=$itable
|
|
|
14
|
|
|
15 --p-dn=$pdn
|
|
|
16
|
|
|
17 --p-mindiffs=$pmindiffs
|
|
|
18
|
|
|
19 --p-mindiv=$pmindiv
|
|
|
20
|
|
|
21 --p-minh=$pminh
|
|
|
22
|
|
|
23 --p-xn=$pxn
|
|
|
24
|
|
|
25 --o-chimeras=ochimeras
|
|
|
26
|
|
|
27 --o-nonchimeras=ononchimeras
|
|
|
28
|
|
|
29 --o-stats=ostats
|
|
|
30
|
|
|
31 #if str($examples) != 'None':
|
|
|
32 --examples=$examples
|
|
|
33 #end if
|
|
|
34
|
|
|
35 ;
|
|
|
36 cp ostats.qza $ostats
|
|
|
37
|
|
|
38 ]]></command>
|
|
|
39 <inputs>
|
|
|
40 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data" />
|
|
|
41 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data" />
|
|
|
42 <param label="--p-dn: NUMBER No vote pseudo-count, corresponding to the Range(0.0, None) parameter n in the chimera scoring function. [default: 1.4]" min="0.0" name="pdn" optional="True" type="float" value="1.4" />
|
|
|
43 <param label="--p-mindiffs: INTEGER Minimum number of differences per segment. Range(1, None) [default: 3]" min="1" name="pmindiffs" optional="True" type="integer" value="3" />
|
|
|
44 <param label="--p-mindiv: NUMBER Minimum divergence from closest parent. Range(0.0, None) [default: 0.8]" min="0.0" name="pmindiv" optional="True" type="float" value="0.8" />
|
|
|
45 <param exclude_max="False" label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" max="1.0" min="0.0" name="pminh" optional="True" type="float" value="0.28" />
|
|
|
46 <param exclude_min="True" label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" max="20.0" min="1.0" name="pxn" optional="True" type="float" value="8.0" />
|
|
|
47 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
|
|
|
48
|
|
|
49 </inputs>
|
|
|
50
|
|
|
51 <outputs>
|
|
|
52 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras" />
|
|
|
53 <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras" />
|
|
|
54 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
|
|
|
55
|
|
|
56 </outputs>
|
|
|
57
|
|
|
58 <help><![CDATA[
|
|
|
59 De novo chimera filtering with vsearch.
|
|
|
60 ###############################################################
|
|
|
61
|
|
|
62 Apply the vsearch uchime_denovo method to identify chimeric feature
|
|
|
63 sequences. The results of this method can be used to filter chimeric
|
|
|
64 features from the corresponding feature table. For additional details,
|
|
|
65 please refer to the vsearch documentation.
|
|
|
66
|
|
|
67 Parameters
|
|
|
68 ----------
|
|
|
69 sequences : FeatureData[Sequence]
|
|
|
70 The feature sequences to be chimera-checked.
|
|
|
71 table : FeatureTable[Frequency]
|
|
|
72 Feature table (used for computing total feature abundances).
|
|
|
73 dn : Float % Range(0.0, None), optional
|
|
|
74 No vote pseudo-count, corresponding to the parameter n in the chimera
|
|
|
75 scoring function.
|
|
|
76 mindiffs : Int % Range(1, None), optional
|
|
|
77 Minimum number of differences per segment.
|
|
|
78 mindiv : Float % Range(0.0, None), optional
|
|
|
79 Minimum divergence from closest parent.
|
|
|
80 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
|
|
|
81 Minimum score (h). Increasing this value tends to reduce the number of
|
|
|
82 false positives and to decrease sensitivity.
|
|
|
83 xn : Float % Range(1.0, None, inclusive_start=False), optional
|
|
|
84 No vote weight, corresponding to the parameter beta in the scoring
|
|
|
85 function.
|
|
|
86
|
|
|
87 Returns
|
|
|
88 -------
|
|
|
89 chimeras : FeatureData[Sequence]
|
|
|
90 The chimeric sequences.
|
|
|
91 nonchimeras : FeatureData[Sequence]
|
|
|
92 The non-chimeric sequences.
|
|
|
93 stats : UchimeStats
|
|
|
94 Summary statistics from chimera checking.
|
|
|
95 ]]></help>
|
|
|
96 <macros>
|
|
|
97 <import>qiime_citation.xml</import>
|
|
|
98 </macros>
|
|
|
99 <expand macro="qiime_citation"/>
|
|
|
100 </tool> |
