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comparison qiime2/qiime_vsearch_uchime-ref.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-ref" name="qiime vsearch uchime-ref" version="2019.4">
3 <description> - Reference-based 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-ref
9
10 --i-sequences=$isequences
11 --i-table=$itable
12 --i-reference-sequences=$ireferencesequences
13
14 #if $pdn:
15 --p-dn=$pdn
16 #end if
17
18 #if $pmindiffs:
19 --p-mindiffs=$pmindiffs
20 #end if
21
22 #if $pmindiv:
23 --p-mindiv=$pmindiv
24 #end if
25
26 #if $pminh:
27 --p-minh=$pminh
28 #end if
29
30 #if $pxn:
31 --p-xn=$pxn
32 #end if
33
34 #set $pthreads = '${GALAXY_SLOTS:-4}'
35 #if str($pthreads):
36 --p-threads="$pthreads"
37 #end if
38
39 --o-chimeras=ochimeras
40 --o-nonchimeras=ononchimeras
41 --o-stats=ostats
42 ;
43 cp ochimeras.qza $ochimeras;
44 cp ononchimeras.qza $ononchimeras;
45 cp ostats.qza $ostats
46 ]]></command>
47 <inputs>
48 <param format="qza,no_unzip.zip" label="--i-sequences: ARTIFACT FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
49 <param format="qza,no_unzip.zip" label="--i-table: ARTIFACT FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data"/>
50 <param format="qza,no_unzip.zip" label="--i-reference-sequences: ARTIFACT FeatureData[Sequence] The non-chimeric reference sequences. [required]" name="ireferencesequences" optional="False" type="data"/>
51 <param label="--p-dn: NUMBER No vote pseudo-count, corresponding to the Range(0.0, None) parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" min="0" value="1.4"/>
52 <param label="--p-mindiffs: INTEGER Minimum number of differences per segment. Range(1, None) [default: 3]" name="pmindiffs" optional="True" type="integer" min="1" value="3"/>
53 <param label="--p-mindiv: NUMBER Minimum divergence from closest parent. Range(0.0, None) [default: 0.8]" name="pmindiv" optional="True" type="float" min="0" value="0.8"/>
54 <param label="--p-minh: PROPORTION Range(0.0, 1.0, inclusive_end=True) Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" name="pminh" optional="True" type="float" min="0" max="1" exclude_max="False" value="0.28"/>
55 <param label="--p-xn: NUMBER Range(1.0, None, inclusive_start=False) No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" name="pxn" optional="True" type="float" min="1" exclude_min="True" value="8.0"/>
56 </inputs>
57 <outputs>
58 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
59 <data format="qza" label="${tool.name} on ${on_string}: nonchimeras.qza" name="ononchimeras"/>
60 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
61 </outputs>
62 <help><![CDATA[
63 Reference-based chimera filtering with vsearch.
64 ###############################################
65
66 Apply the vsearch uchime_ref method to identify chimeric feature sequences.
67 The results of this method can be used to filter chimeric features from the
68 corresponding feature table. For additional details, please refer to the
69 vsearch documentation.
70
71 Parameters
72 ----------
73 sequences : FeatureData[Sequence]
74 The feature sequences to be chimera-checked.
75 table : FeatureTable[Frequency]
76 Feature table (used for computing total feature abundances).
77 reference_sequences : FeatureData[Sequence]
78 The non-chimeric reference sequences.
79 dn : Float % Range(0.0, None), optional
80 No vote pseudo-count, corresponding to the parameter n in the chimera
81 scoring function.
82 mindiffs : Int % Range(1, None), optional
83 Minimum number of differences per segment.
84 mindiv : Float % Range(0.0, None), optional
85 Minimum divergence from closest parent.
86 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
87 Minimum score (h). Increasing this value tends to reduce the number of
88 false positives and to decrease sensitivity.
89 xn : Float % Range(1.0, None, inclusive_start=False), optional
90 No vote weight, corresponding to the parameter beta in the scoring
91 function.
92 threads : Int % Range(0, 256, inclusive_end=True), optional
93 The number of threads to use for computation. Passing 0 will launch one
94 thread per CPU core.
95
96 Returns
97 -------
98 chimeras : FeatureData[Sequence]
99 The chimeric sequences.
100 nonchimeras : FeatureData[Sequence]
101 The non-chimeric sequences.
102 stats : UchimeStats
103 Summary statistics from chimera checking.
104 ]]></help>
105 <macros>
106 <import>qiime_citation.xml</import>
107 </macros>
108 <expand macro="qiime_citation"/>
109 </tool>