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comparison qiime2/qiime_vsearch_uchime-denovo.xml @ 0:51b9b6b57732 draft

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author florianbegusch
date Thu, 24 May 2018 05:21:07 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_uchime-denovo" name="qiime vsearch uchime-denovo" version="2018.4">
3 <description> - De novo chimera filtering with vsearch.</description>
4 <requirements>
5 <requirement type="package" version="2018.4">qiime2</requirement>
6 </requirements>
7 <command>
8 <![CDATA[
9 qiime vsearch uchime-denovo --i-table=$itable --i-sequences=$isequences
10
11 #if $pdn:
12 --p-dn=$pdn
13 #end if
14 --o-nonchimeras=ononchimeras --o-stats=ostats --o-chimeras=ochimeras
15 #if $pmindiffs:
16 --p-mindiffs=$pmindiffs
17 #end if
18
19 #if $pminh:
20 --p-minh=$pminh
21 #end if
22
23 #if str($cmdconfig) != 'None':
24 --cmd-config=$cmdconfig
25 #end if
26
27 #if $pmindiv:
28 --p-mindiv=$pmindiv
29 #end if
30
31 #if $pxn:
32 --p-xn=$pxn
33 #end if
34 ;
35 cp ononchimeras.qza $ononchimeras;
36 cp ostats.qza $ostats;
37 cp ochimeras.qza $ochimeras;
38 ]]>
39 </command>
40 <inputs>
41 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
42 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data"/>
43
44 <param label="--p-dn: No vote pseudo-count, corresponding to the parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" value="1.4"/>
45
46 <param label="--p-mindiffs: Minimum number of differences per segment. [default: 3]" name="pmindiffs" optional="True" type="integer" value="3"/>
47 <param label="--p-mindiv: Minimum divergence from closest parent. [default: 0.8]" name="pmindiv" optional="True" type="float" value="0.8"/>
48 <param label="--p-minh: Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" name="pminh" optional="True" type="float" value="0.28"/>
49
50 <param label="--p-xn: No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" name="pxn" optional="True" type="float" value="8.0"/>
51
52 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
53 </inputs>
54 <outputs>
55 <data format="qza" label="${tool.name} on ${on_string}: non-chimeras.qza" name="ononchimeras"/>
56 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
57 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
58 </outputs>
59 <help>
60 <![CDATA[
61 De novo chimera filtering with vsearch.
62 ----------------------------------------
63
64 Apply the vsearch uchime_denovo method to identify chimeric feature
65 sequences. The results of this method can be used to filter chimeric
66 features from the corresponding feature table. For additional details,
67 please refer to the vsearch documentation.
68
69 Parameters
70 ----------
71 sequences : FeatureData[Sequence]
72 The feature sequences to be chimera-checked.
73 table : FeatureTable[Frequency]
74 Feature table (used for computing total feature abundances).
75 dn : Float % Range(0.0, None), optional
76 No vote pseudo-count, corresponding to the parameter n in the chimera
77 scoring function.
78 mindiffs : Int % Range(1, None), optional
79 Minimum number of differences per segment.
80 mindiv : Float % Range(0.0, None), optional
81 Minimum divergence from closest parent.
82 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
83 Minimum score (h). Increasing this value tends to reduce the number of
84 false positives and to decrease sensitivity.
85 xn : Float % Range(1.0, None, inclusive_start=False), optional
86 No vote weight, corresponding to the parameter beta in the scoring
87 function.
88
89 Returns
90 -------
91 chimeras : FeatureData[Sequence]
92 The chimeric sequences.
93 nonchimeras : FeatureData[Sequence]
94 The non-chimeric sequences.
95 stats : UchimeStats
96 Summary statistics from chimera checking.
97 ]]>
98 </help>
99 <macros>
100 <import>qiime_citation.xml</import>
101 </macros>
102 <expand macro="qiime_citation" />
103 </tool>