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comparison qiime_vsearch_uchime-ref.xml @ 0:09b7bcb72fa7 draft

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author florianbegusch
date Thu, 24 May 2018 02:11:44 -0400
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1 <?xml version="1.0" ?>
2 <tool id="qiime_vsearch_uchime-ref" name="qiime vsearch uchime-ref" version="2018.4">
3 <description> - Reference-based 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-ref --i-table=$itable --i-sequences=$isequences --i-reference-sequences=$ireferencesequences --o-nonchimeras=ononchimeras --o-stats=ostats
10
11 #if $pmindiffs:
12 --p-mindiffs=$pmindiffs
13 #end if
14
15 #set $pthreads = '${GALAXY_SLOTS:-4}'
16
17 #if str($pthreads):
18 --p-threads="$pthreads"
19 #end if
20
21
22 #if $pdn:
23 --p-dn=$pdn
24 #end if
25 --o-chimeras=ochimeras
26 #if str($cmdconfig) != 'None':
27 --cmd-config=$cmdconfig
28 #end if
29
30 #if $pminh:
31 --p-minh=$pminh
32 #end if
33
34 #if $pmindiv:
35 --p-mindiv=$pmindiv
36 #end if
37
38 #if $pxn:
39 --p-xn=$pxn
40 #end if
41 ;
42 cp ononchimeras.qza $ononchimeras;
43 cp ostats.qza $ostats;
44 cp ochimeras.qza $ochimeras
45 ]]>
46 </command>
47 <inputs>
48 <param format="qza,no_unzip.zip" label="--i-sequences: FeatureData[Sequence] The feature sequences to be chimera-checked. [required]" name="isequences" optional="False" type="data"/>
49 <param format="qza,no_unzip.zip" label="--i-table: FeatureTable[Frequency] Feature table (used for computing total feature abundances). [required]" name="itable" optional="False" type="data"/>
50 <param format="qza,no_unzip.zip" label="--i-reference-sequences: FeatureData[Sequence] The non-chimeric reference sequences. [required]" name="ireferencesequences" optional="False" type="data"/>
51
52 <param label="--p-dn: No vote pseudo-count, corresponding to the parameter n in the chimera scoring function. [default: 1.4]" name="pdn" optional="True" type="float" value="1.4"/>
53
54 <param label="--p-mindiffs: Minimum number of differences per segment. [default: 3]" name="pmindiffs" optional="True" type="integer" value="3"/>
55 <param label="--p-mindiv: Minimum divergence from closest parent. [default: 0.8]" name="pmindiv" optional="True" type="float" value="0.8"/>
56 <param label="--p-minh: Minimum score (h). Increasing this value tends to reduce the number of false positives and to decrease sensitivity. [default: 0.28]" name="pminh" optional="True" type="float" value="0.28"/>
57
58 <param label="--p-xn: No vote weight, corresponding to the parameter beta in the scoring function. [default: 8.0]" name="pxn" optional="True" type="float" value="8.0"/>
59
60 <param label="--cmd-config: Use config file for command options" name="cmdconfig" optional="True" type="data"/>
61 </inputs>
62 <outputs>
63 <data format="qza" label="${tool.name} on ${on_string}: non-chimeras.qza" name="ononchimeras"/>
64 <data format="qza" label="${tool.name} on ${on_string}: stats.qza" name="ostats"/>
65 <data format="qza" label="${tool.name} on ${on_string}: chimeras.qza" name="ochimeras"/>
66 </outputs>
67 <help>
68 <![CDATA[
69 Reference-based chimera filtering with vsearch.
70 ------------------------------------------------
71
72 Apply the vsearch uchime_ref method to identify chimeric feature sequences.
73 The results of this method can be used to filter chimeric features from the
74 corresponding feature table. For additional details, please refer to the
75 vsearch documentation.
76
77 Parameters
78 ----------
79 sequences : FeatureData[Sequence]
80 The feature sequences to be chimera-checked.
81 table : FeatureTable[Frequency]
82 Feature table (used for computing total feature abundances).
83 reference_sequences : FeatureData[Sequence]
84 The non-chimeric reference sequences.
85 dn : Float % Range(0.0, None), optional
86 No vote pseudo-count, corresponding to the parameter n in the chimera
87 scoring function.
88 mindiffs : Int % Range(1, None), optional
89 Minimum number of differences per segment.
90 mindiv : Float % Range(0.0, None), optional
91 Minimum divergence from closest parent.
92 minh : Float % Range(0.0, 1.0, inclusive_end=True), optional
93 Minimum score (h). Increasing this value tends to reduce the number of
94 false positives and to decrease sensitivity.
95 xn : Float % Range(1.0, None, inclusive_start=False), optional
96 No vote weight, corresponding to the parameter beta in the scoring
97 function.
98
99 Returns
100 -------
101 chimeras : FeatureData[Sequence]
102 The chimeric sequences.
103 nonchimeras : FeatureData[Sequence]
104 The non-chimeric sequences.
105 stats : UchimeStats
106 Summary statistics from chimera checking.
107 ]]>
108 </help>
109 </tool>