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comparison chimera.xml @ 0:fae6527990af draft

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Imported from capsule None
author iuc
date Thu, 21 May 2015 03:58:09 -0400
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children f29e21388219
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-1:000000000000 0:fae6527990af
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>