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comparison qiime2/qiime_vsearch_uchime-ref.xml @ 29:3ba9833030c1 draft

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author florianbegusch
date Fri, 04 Sep 2020 13:12:49 +0000
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1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref"
3 version="2020.8">
4 <description>Reference-based 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-ref
10
11 --i-sequences=$isequences
12
13 --i-table=$itable
14
15 --i-reference-sequences=$ireferencesequences
16
17 --p-dn=$pdn
18
19 --p-mindiffs=$pmindiffs
20
21 --p-mindiv=$pmindiv
22
23 --p-minh=$pminh
24
25 --p-xn=$pxn
26
27 --p-threads=$pthreads
28
29 --o-chimeras=ochimeras
30
31 --o-nonchimeras=ononchimeras
32
33 --o-stats=ostats
34
35 #if str($examples) != 'None':
36 --examples=$examples
37 #end if
38
39 ;
40 cp ostats.qza $ostats
41
42 ]]></command>
43 <inputs>
44 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data" />
45 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data" />
46 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The non-chimeric reference sequences. [required]" name="ireferencesequences" optional="False" type="data" />
47 <param label="--p-dn: NUMBER No vote pseudo-count, corresponding to the Range(0.0, None) parameter n in the chimera scoring function. [default: 1.4]" min="0.0" name="pdn" optional="True" type="float" value="1.4" />
48 <param label="--p-mindiffs: INTEGER Minimum number of differences per segment. Range(1, None) [default: 3]" min="1" name="pmindiffs" optional="True" type="integer" value="3" />
49 <param label="--p-mindiv: NUMBER Minimum divergence from closest parent. Range(0.0, None) [default: 0.8]" min="0.0" name="pmindiv" optional="True" type="float" value="0.8" />
50 <param exclude_max="False" label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" max="1.0" min="0.0" name="pminh" optional="True" type="float" value="0.28" />
51 <param exclude_min="True" label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" max="20.0" min="1.0" name="pxn" optional="True" type="float" value="8.0" />
52 <param label="--examples: Show usage examples and exit." name="examples" optional="False" type="data" />
53
54 </inputs>
55
56 <outputs>
57 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras" />
58 <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras" />
59 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats" />
60
61 </outputs>
62
63 <help><![CDATA[
64 Reference-based chimera filtering with vsearch.
65 ###############################################################
66
67 Apply the vsearch uchime_ref method to identify chimeric feature sequences.
68 The results of this method can be used to filter chimeric features from the
69 corresponding feature table. For additional details, please refer to the
70 vsearch documentation.
71
72 Parameters
73 ----------
74 sequences : FeatureData[Sequence]
75 The feature sequences to be chimera-checked.
76 table : FeatureTable[Frequency]
77 Feature table (used for computing total feature abundances).
78 reference_sequences : FeatureData[Sequence]
79 The non-chimeric reference sequences.
80 dn : Float % Range(0.0, None), optional
81 No vote pseudo-count, corresponding to the parameter n in the chimera
82 scoring function.
83 mindiffs : Int % Range(1, None), optional
84 Minimum number of differences per segment.
85 mindiv : Float % Range(0.0, None), optional
86 Minimum divergence from closest parent.
87 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
88 Minimum score (h). Increasing this value tends to reduce the number of
89 false positives and to decrease sensitivity.
90 xn : Float % Range(1.0, None, inclusive_start=False), optional
91 No vote weight, corresponding to the parameter beta in the scoring
92 function.
93 threads : Int % Range(0, 256, inclusive_end=True), optional
94 The number of threads to use for computation. Passing 0 will launch one
95 thread per CPU core.
96
97 Returns
98 -------
99 chimeras : FeatureData[Sequence]
100 The chimeric sequences.
101 nonchimeras : FeatureData[Sequence]
102 The non-chimeric sequences.
103 stats : UchimeStats
104 Summary statistics from chimera checking.
105 ]]></help>
106 <macros>
107 <import>qiime_citation.xml</import>
108 </macros>
109 <expand macro="qiime_citation"/>
110 </tool>