|
0
|
1 <tool id="vsearch_chimera_detection" name="VSearch chimera detection" version="@VERSION@.0">
|
|
|
2 <description></description>
|
|
|
3 <macros>
|
|
|
4 <import>vsearch_macros.xml</import>
|
|
|
5 </macros>
|
|
|
6 <expand macro="requirements" />
|
|
|
7 <expand macro="stdio" />
|
|
|
8 <expand macro="version_command" />
|
|
|
9 <command>
|
|
|
10 <![CDATA[
|
|
|
11 vsearch
|
|
|
12 @GENERAL@
|
|
|
13 --abskew $abskew
|
|
|
14 --chimeras $outfile
|
|
|
15 --dn $dn
|
|
|
16 --mindiffs $mindiffs
|
|
|
17 --mindiv $mindiv
|
|
|
18 --minh $minh
|
|
|
19 --xn $xn
|
|
|
20 $self_param
|
|
|
21 $selfid_param
|
|
|
22 #if $detection_mode.detection_mode_select == 'denovo':
|
|
|
23 --uchime_denovo $detection_mode.infile_denovo
|
|
|
24 #else:
|
|
|
25 --uchime_ref $detection_mode.infile_reference
|
|
|
26 --db $detection_mode.db
|
|
|
27 #end if
|
|
|
28
|
|
|
29 #if 'nonchimeras' in str($outputs):
|
|
|
30 --nonchimeras $nonchimeras
|
|
|
31 #end if
|
|
|
32 #if 'uchimealns' in str($outputs):
|
|
|
33 --uchimealns $uchimealns
|
|
|
34 #end if
|
|
|
35 #if 'uchimeout' in str($outputs):
|
|
|
36 --uchimeout $uchimeout
|
|
|
37 #end if
|
|
|
38
|
|
|
39 ]]>
|
|
|
40 </command>
|
|
|
41 <inputs>
|
|
|
42 <conditional name="detection_mode">
|
|
|
43 <param name="detection_mode_select" type="select" label="Detect chimeras" help="">
|
|
|
44 <option value="denovo">de novo</option>
|
|
|
45 <option value="reference">using a reference database</option>
|
|
|
46 </param>
|
|
|
47 <when value="denovo">
|
|
|
48 <param name="infile_denovo" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_denovo)" />
|
|
|
49 </when>
|
|
|
50 <when value="reference">
|
|
|
51 <param name="infile_reference" type="data" format="fasta" label="Select your FASTA file" help="(--uchime_ref)" />
|
|
|
52 <param name="db" type="data" format="fasta" label="Select your reference database" help="(--db)" />
|
|
|
53 </when>
|
|
|
54 </conditional>
|
|
|
55
|
|
|
56 <param name="abskew" type="float" value="2.0" label="Minimal abundance ratio of parent vs chimera"
|
|
|
57 help="(--abskew)"/>
|
|
|
58 <param name="dn" type="float" value="1.4" label="'no' vote pseudo count"
|
|
|
59 help="(--dn)"/>
|
|
|
60 <param name="xn" type="float" value="8.0" label="'no' vote weight"
|
|
|
61 help="(--xn)"/>
|
|
|
62 <param name="mindiffs" type="integer" value="3" label="Minimum number of differences in segment"
|
|
|
63 help="(--mindiffs)"/>
|
|
|
64 <param name="mindiv" type="float" value="0.8" label="Minimum divergence from closest parent"
|
|
|
65 help="(--mindiv)"/>
|
|
|
66 <param name="minh" type="float" value="0.28" label="Minimum score"
|
|
|
67 help="(--minh)"/>
|
|
|
68
|
|
|
69 <expand macro="self_and_selfid" />
|
|
|
70
|
|
|
71 <param name="outputs" type="select" multiple="True" optional="True"
|
|
|
72 label="Select output formats" help="(--qmask)">
|
|
|
73 <option value="nonchimeras">Non-chimeric sequences (--nonchimeras)</option>
|
|
|
74 <option value="uchimealns">Chimera alignments (--uchimealns)</option>
|
|
|
75 <option value="uchimeout">Chimera info to tab-separated (--uchimeout)</option>
|
|
|
76 </param>
|
|
|
77
|
|
|
78 </inputs>
|
|
|
79 <outputs>
|
|
|
80 <data name="outfile" format="fasta" label="${tool.name} on ${on_string}" />
|
|
|
81 <data name="nonchimeras" format="fasta" label="${tool.name} on ${on_string}: Non Chimera">
|
|
|
82 <filter>'nonchimeras' in outputs</filter>
|
|
|
83 </data>
|
|
|
84 <data name="uchimealns" format="fasta" label="${tool.name} on ${on_string}: Chimera Alignments">
|
|
|
85 <filter>'uchimealns' in outputs</filter>
|
|
|
86 </data>
|
|
|
87 <data name="uchimeout" format="tabular" label="${tool.name} on ${on_string}: Chimera Information">
|
|
|
88 <filter>'uchimeout' in outputs</filter>
|
|
|
89 </data>
|
|
|
90 </outputs>
|
|
|
91 <tests>
|
|
|
92 <test>
|
|
|
93 <param name="detection_mode_select" value="denovo"/>
|
|
|
94 <param name="infile_denovo" value="PR2-18S-rRNA-V4.derep.fsa.bz2" ftype="fasta" />
|
|
|
95 <param name="outputs" value="uchimeout"/>
|
|
|
96 <output name="outfile" file="chimera_result1.fasta" ftype="fasta" />
|
|
|
97 <output name="uchimeout" file="chimera_uchimeout_result1.tabular" ftype="tabular" />
|
|
|
98 </test>
|
|
|
99 </tests>
|
|
|
100 <help>
|
|
|
101 <![CDATA[
|
|
|
102 **What it does**
|
|
|
103
|
|
|
104 Sequence chimera detection based on a different scoring functions.
|
|
|
105
|
|
|
106 Chimera detection options
|
|
|
107 --abskew REAL min abundance ratio of parent vs chimera (2.0)
|
|
|
108 --alignwidth INT width of alignment in uchimealn output (80)
|
|
|
109 --chimeras FILENAME output chimeric sequences to file
|
|
|
110 --db FILENAME reference database for --uchime_ref
|
|
|
111 --dn REAL 'no' vote pseudo-count (1.4)
|
|
|
112 --mindiffs INT minimum number of differences in segment (3)
|
|
|
113 --mindiv REAL minimum divergence from closest parent (0.8)
|
|
|
114 --minh REAL minimum score (0.28)
|
|
|
115 --nonchimeras FILENAME output non-chimeric sequences to file
|
|
|
116 --self exclude identical labels for --uchime_ref
|
|
|
117 --selfid exclude identical sequences for --uchime_ref
|
|
|
118 --uchime_denovo FILENAME detect chimeras de novo
|
|
|
119 --uchime_ref FILENAME detect chimeras using a reference database
|
|
|
120 --uchimealns FILENAME output chimera alignments to file
|
|
|
121 --uchimeout FILENAME output to chimera info to tab-separated file
|
|
|
122 --uchimeout5 make output compatible with uchime version 5
|
|
|
123 --xn REAL 'no' vote weight (8.0)
|
|
|
124
|
|
|
125 @EXTERNAL_DOCUMENTATION@
|
|
|
126
|
|
|
127 -------
|
|
|
128
|
|
|
129 @REFERENCES@
|
|
|
130
|
|
|
131
|
|
|
132 ]]>
|
|
|
133 </help>
|
|
|
134 <expand macro="citations" />
|
|
|
135 </tool>
|
