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comparison qiime2/qiime_vsearch_uchime-denovo.xml @ 0:370e0b6e9826 draft

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author florianbegusch
date Wed, 17 Jul 2019 03:05:17 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_uchime-denovo" name="qiime vsearch uchime-denovo" version="2019.4">
3 <description> - De novo chimera filtering with vsearch.</description>
4 <requirements>
5 <requirement type="package" version="2019.4">qiime2</requirement>
6 </requirements>
7 <command><![CDATA[
8 qiime vsearch uchime-denovo
9
10 --i-sequences=$isequences
11 --i-table=$itable
12
13 #if $pdn:
14 --p-dn=$pdn
15 #end if
16
17 #if $pmindiffs:
18 --p-mindiffs=$pmindiffs
19 #end if
20
21 #if $pmindiv:
22 --p-mindiv=$pmindiv
23 #end if
24
25 #if $pminh:
26 --p-minh=$pminh
27 #end if
28
29 #if $pxn:
30 --p-xn=$pxn
31 #end if
32
33 --o-chimeras=ochimeras
34 --o-nonchimeras=ononchimeras
35 --o-stats=ostats
36 ;
37 cp ochimeras.qza $ochimeras;
38 cp ononchimeras.qza $ononchimeras;
39 cp ostats.qza $ostats
40 ]]></command>
41 <inputs>
42 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
43 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data"/>
44
45 <param label="--p-dn: NUMBER No vote pseudo-count, corresponding to the Range(0.0, None) parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" min="0" value="1.4"/>
46 <param label="--p-mindiffs: INTEGER Minimum number of differences per segment. Range(1, None) [default: 3]" name="pmindiffs" optional="True" type="integer" min="1" value="3"/>
47 <param label="--p-mindiv: NUMBER Minimum divergence from closest parent. Range(0.0, None) [default: 0.8]" name="pmindiv" optional="True" type="float" min="0" value="0.8"/>
48 <param label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" name="pminh" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.28"/>
49 <param label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" name="pxn" optional="True" type="float" min="1" exclude_max="True" value="8.0"/>
50 </inputs>
51 <outputs>
52 <data format="qza" label="${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 </outputs>
56 <help><![CDATA[
57 De novo chimera filtering with vsearch.
58 #######################################
59
60 Apply the vsearch uchime_denovo method to identify chimeric feature
61 sequences. The results of this method can be used to filter chimeric
62 features from the corresponding feature table. For additional details,
63 please refer to the vsearch documentation.
64
65 Parameters
66 ----------
67 sequences : FeatureData[Sequence]
68 The feature sequences to be chimera-checked.
69 table : FeatureTable[Frequency]
70 Feature table (used for computing total feature abundances).
71 dn : Float % Range(0.0, None), optional
72 No vote pseudo-count, corresponding to the parameter n in the chimera
73 scoring function.
74 mindiffs : Int % Range(1, None), optional
75 Minimum number of differences per segment.
76 mindiv : Float % Range(0.0, None), optional
77 Minimum divergence from closest parent.
78 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
79 Minimum score (h). Increasing this value tends to reduce the number of
80 false positives and to decrease sensitivity.
81 xn : Float % Range(1.0, None, inclusive_start=False), optional
82 No vote weight, corresponding to the parameter beta in the scoring
83 function.
84
85 Returns
86 -------
87 chimeras : FeatureData[Sequence]
88 The chimeric sequences.
89 nonchimeras : FeatureData[Sequence]
90 The non-chimeric sequences.
91 stats : UchimeStats
92 Summary statistics from chimera checking.
93 ]]></help>
94 <macros>
95 <import>qiime_citation.xml</import>
96 </macros>
97 <expand macro="qiime_citation"/>
98 </tool>