Mercurial > repos > iuc > hmmer_hmmsearch

annotate macros.xml.orig @ 11:405dd85a9408 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
author iuc
date Tue, 31 Aug 2021 08:43:59 +0000
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
11
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
1 <?xml version="1.0"?>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
2 <macros>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
3 <xml name="requirements">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
4 <requirements>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
5 <requirement type="package" version="@TOOL_VERSION@">hmmer</requirement>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
6 <yield/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
7 </requirements>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
8 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
9 <<<<<<< HEAD
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
10 <xml name="bio_tools">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
11 <xrefs>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
12 <xref type="bio.tools">gemini</xref>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
13 </xrefs>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
14 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
15 =======
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
16 <xml name="bio_tools">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
17 <xrefs>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
18 <xref type="bio.tools">hmmer3</xref>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
19 </xrefs>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
20 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
21 >>>>>>> 5f65381bd (fix id of hmmer3)
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
22 <token name="@TOOL_VERSION@">3.3.2</token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
23 <xml name="stdio">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
24 <stdio>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
25 <!-- Anything other than zero is an error -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
26 <exit_code range="1:"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
27 <exit_code range=":-1"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
28 <!-- In case the return code has not been set propery check stderr too -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
29 <regex match="Error:"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
30 <regex match="Exception:"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
31 </stdio>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
32 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
33 <token name="@THRESHOLDS@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
34 -E $E
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
35 --domE $domE
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
36
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
37 #if str($T):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
38 -T $T
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
39 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
40
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
41 #if str($domT):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
42 --domT $domT
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
43 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
44
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
45 #if str($incE):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
46 --incE $incE
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
47 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
48
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
49 #if str($incdomE):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
50 --incdomE $incdomE
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
51 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
52
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
53 #if str($incT):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
54 --incT $incT
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
55 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
56
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
57 #if str($incdomT):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
58 --incdomT $incdomT
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
59 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
60 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
61 <xml name="thresholds_xml">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
62 <!-- Options controlling reporting thresholds -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
63 <param argument="-E" type="float" min="0" value="10.0" label="report sequences &lt;= this E-Value threshold in output" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
64 <param argument="--domE" type="float" min="0" value="10.0" label="report domains &lt;= this E-Value threshold in output" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
65 <param argument="-T" type="float" optional="true" label="report sequences &gt;= this score threshold in output" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
66 <param argument="--domT" type="float" optional="true" label="report domains &gt;= this score threshold in output" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
67 <!-- Options controlling inclusion (significance) thresholds -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
68 <param argument="--incE" type="float" optional="true" label="consider sequences &lt;= this E-Value threshold as significant" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
69 <param argument="--incdomE" type="float" optional="true" label="consider domains &lt;= this E-Value threshold as significant" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
70 <param argument="--incT" type="float" optional="true" label="consider sequences &gt;= this score threshold as significant" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
71 <param argument="--incdomT" type="float" optional="true" label="consider domains &gt;= this score threshold as significant" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
72 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
73 <token name="@THRESHOLDS_NODOM@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
74 -E $E
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
75
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
76 #if str($T):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
77 -T $T
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
78 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
79
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
80 #if str($incE):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
81 --incE $incE
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
82 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
83
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
84 #if str($incT):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
85 --incT $incT
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
86 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
87 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
88 <xml name="thresholds_nodom">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
89 <!-- Options controlling reporting thresholds -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
90 <param argument="-E" type="float" min="0" value="10.0" label="report sequences &lt;= this E-Value threshold in output" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
91 <param argument="-T" type="float" optional="true" label="report sequences &gt;= this score threshold in output" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
92 <!-- Options controlling inclusion (significance) thresholds -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
93 <param argument="--incE" type="float" optional="true" label="consider sequences &lt;= this E-Value threshold as significant" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
94 <param argument="--incT" type="float" optional="true" label="consider sequences &gt;= this score threshold as significant" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
95 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
96 <token name="@ACCEL_HEUR@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
97 $max
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
98 --F1 $F1
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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99 --F2 $F2
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
100 --F3 $F3
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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101 $nobias
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
102 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
103 <xml name="accel_heur_xml">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
104 <!-- Options controlling acceleration heuristics -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
105 <param argument="--max" type="boolean" truevalue="--max" falsevalue="" label="Turn all heuristic filters off (less speed, more power)" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
106 <param argument="--F1" type="float" value="0.02" label="Stage 1 (MSV) threshold: promote hits w/ P &lt;= F1" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
107 <param argument="--F2" type="float" value="1e-3" label="Stage 2 (Vit) threshold: promote hits w/ P &lt;= F2" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
108 <param argument="--F3" type="float" value="1e-5" label="Stage 3 (Fwd) threshold: promote hits w/ P &lt;= F3" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
109 <param argument="--nobias" type="boolean" truevalue="--nobias" falsevalue="" label="Turn off composition bias filter" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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110 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
111 <token name="@EVAL_CALIB@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
112 --EmL $EmL
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
113 --EmN $EmN
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
114 --EvL $EvL
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
115 --EvN $EvN
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
116 --EfL $EfL
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
117 --EfN $EfN
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
118 --Eft $Eft
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
119 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
120 <xml name="eval_calib_xml">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
121 <!-- Control of E-value calibration -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
122 <param argument="--EmL" type="integer" min="1" value="200" label="Length of sequences for MSV Gumbel mu fit" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
123 <param argument="--EmN" type="integer" min="1" value="200" label="Number of sequences for MSV Gumbel mu fit" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
124 <param argument="--EvL" type="integer" min="1" value="200" label="Length of sequences for Viterbi Gumbel mu fit" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
125 <param argument="--EvN" type="integer" min="1" value="200" label="Number of sequences for Viterbi Gumbel mu fit" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
126 <param argument="--EfL" type="integer" min="1" value="100" label="Length of sequences for Forward exp tail tau fit" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
127 <param argument="--EfN" type="integer" min="1" value="200" label="Number of sequences for Forward exp tail tau fit" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
128 <param argument="--Eft" type="float" min="0" max="1" value="0.04" label="tail mass for Forward exponential tail tau fit" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
129 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
130 <token name="@OFORMAT_WITH_OPTS@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
131 #if $oformat:
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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132 #for o in str($oformat).split(','):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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133 --$o '$getVar($o, 'MISSING_OUTPUT'+$o)'
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
134 #end for
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
135 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
136 $acc $noali $notextw
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
137 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
138 <xml name="oformat_with_opts">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
139 <!-- Options directing output -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
140 <param name="oformat" type="select" multiple="true" display="checkboxes" label="Output Formats">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
141 <option value="tblout" selected="true">Table of per-sequence hits (--tblout)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
142 <yield/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
143 </param>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
144 <param argument="--acc" type="boolean" truevalue="--acc" falsevalue="" label="Prefer accessions over names in output" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
145 <param argument="--noali" type="boolean" truevalue="--noali" falsevalue="" label="Don't output alignments, so output is smaller" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
146 <param argument="--notextw" type="boolean" truevalue="--notextw" falsevalue="" label="Unlimited ASCII text output line width" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
147 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
148
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
149 <xml name="oformat_with_opts_dom">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
150 <expand macro="oformat_with_opts">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
151 <option value="domtblout" selected="true">Table of per-domain hits (--domtblout)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
152 <yield/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
153 </expand>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
154 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
155
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
156 <xml name="oformat_with_opts_dom_pfam">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
157 <expand macro="oformat_with_opts_dom">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
158 <option value="pfamtblout" selected="true">Table of hits and domains in Pfam format (--pfamtblout)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
159 </expand>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
160 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
161
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
162 <xml name="oformat_with_opts_dfam_alisc">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
163 <!-- Options directing output -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
164 <expand macro="oformat_with_opts">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
165 <option value="dfamtblout" selected="true">Table of hits in Dfam format (--dfamtblout)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
166 <option value="aliscoresout">Scores for each position in each alignment to file (--aliscoresout)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
167 </expand>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
168 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
169
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
170 <xml name="output" token_tool="">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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171 <data name="output" format="txt" label="@TOOL@ on ${on_string}"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
172 <data name="tblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence hits from HMM matches">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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173 <filter>oformat and 'tblout' in oformat</filter>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
174 </data>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
175 <yield/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
176 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
177 <xml name="output_dom" token_tool="">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
178 <expand macro="output" tool="@TOOL@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
179 <data name="domtblout" format="txt" label="@TOOL@ on ${on_string}: per-domain hits from HMM matches">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
180 <filter>oformat and 'domtblout' in oformat</filter>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
181 </data>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
182 </expand>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
183 <yield/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
184 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
185 <xml name="output_dom_pfam" token_tool="">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
186 <expand macro="output_dom" tool="@TOOL@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
187 <data name="pfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
188 <filter>oformat and 'pfamtblout' in oformat</filter>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
189 </data>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
190 </expand>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
191 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
192 <xml name="output_dfam_alisc" token_tool="" token_ofvar="seqfile" token_invar="seqdb">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
193 <expand macro="output" tool="@TOOL@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
194 <data name="dfamtblout" format="txt" label="@TOOL@ on ${on_string}: per-sequence/per-domain hits from HMM matches">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
195 <filter>oformat and 'dfamtblout' in oformat</filter>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
196 </data>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
197 <data name="aliscoresout" format="txt" label="@TOOL@ on ${on_string}: scores for positional matches">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
198 <filter>oformat and 'aliscoresout' in oformat</filter>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
199 </data>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
200 </expand>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
201 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
202
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
203 <xml name="assert_out" token_tool="">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
204 <assert_contents>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
205 <has_line_matching expression="# @TOOL@.*"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
206 <has_line_matching expression="\[ok\]"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
207 </assert_contents>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
208 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
209
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
210 <xml name="assert_tblout" token_tool="">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
211 <assert_contents>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
212 <has_line_matching expression="# Program: @TOOL@"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
213 <has_line_matching expression="# \[ok\]"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
214 </assert_contents>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
215 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
216
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
217 <xml name="oformat_test">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
218 <param name="notextw" value="true" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
219 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
220 <token name="@HSSI@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
221 #if $hssi.hssi_select == "singlemx":
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
222 --popen $hssi.popen
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
223 --pextend $hssi.pextend
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
224 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
225 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
226 <xml name="hssi">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
227 <!-- Handling single sequence inputs -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
228 <conditional name="hssi">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
229 <param name="hssi_select" type="select" label="Options for handling single sequence inputs">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
230 <option value="false" selected="true">Disable</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
231 <option value="singlemx">Use substitution score matrix for single-sequence inputs</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
232 </param>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
233 <when value="false" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
234 <when value="singlemx">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
235 <param argument="--popen" type="float" min="0.0" max="0.5" value="0.02" label="Gap open probability" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
236 <param argument="--pextend" type="float" min="0.0" max="1.0" value="0.4" label="Gap extend probability" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
237 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
238 <!-- -mx <s> : substitution score matrix (built-in matrices, with -singlemx)-->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
239 <!-- -mxfile <f> : read substitution score matrix from file <f> (with -singlemx)-->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
240 </conditional>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
241 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
242 <token name="@ADDTHREADS@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
243 ##compute the number of ADDITIONAL threads to be used (--cpu)
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
244 addthreads=\${GALAXY_SLOTS:-1} && (( addthreads-- )) &&
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
245 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
246 <token name="@CPU@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
247 --cpu \$addthreads
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
248 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
249 <token name="@SEED@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
250 --seed $seed
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
251 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
252 <xml name="seed">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
253 <param argument="--seed" type="integer" min="0" value="42" label="RNG seed, 0 generates a random seed" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
254 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
255 <xml name="seed_test">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
256 <param name="seed" value="4" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
257 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
258 <token name="@ADV_OPTS@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
259 $nonull2
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
260
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
261 #if str($Z):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
262 -Z $Z
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
263 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
264
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
265 #if str($domZ):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
266 --domZ $domZ
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
267 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
268 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
269 <xml name="adv_opts">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
270 <!-- Other options -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
271 <param argument="--nonull2" type="boolean" truevalue="--nonull2" falsevalue="" label="Turn off biased composition score corrections" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
272 <param argument="-Z" type="integer" optional="true" label="# of comparisons done for E-value calculation" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
273 <param argument="--domZ" type="integer" optional="true" label="# of significant sequences, for domain E-value calculation" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
274 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
275 <token name="@FORMAT_SELECTOR@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
276 $input_format_select
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
277 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
278 <xml name="format_selector">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
279 <param name="input_format_select" type="select" label="Format of sequence and model">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
280 <option value="--amino">Protein</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
281 <option value="--dna">DNA</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
282 <option value="--rna">RNA</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
283 </param>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
284 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
285 <xml name="format_selector_noprot">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
286 <param name="input_format_select" type="select" label="Format of sequence and model">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
287 <option value="--dna">DNA</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
288 <option value="--rna">RNA</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
289 </param>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
290 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
291 <token name="@ARSWS@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
292 $arsws.arsws_select
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
293
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
294 #if $arsws.arsws_select == "--wblosum":
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
295 --wid $arsws.wid
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
296 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
297 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
298 <xml name="arsws">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
299 <!-- Alternative relative sequence weighting strategies -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
300 <conditional name="arsws">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
301 <param name="arsws_select" type="select" label="Alternative relative sequence weighting strategies">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
302 <option value="--wpb" selected="true">Henikoff position-based weights (--wpb)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
303 <option value="--wgsc">Gerstein/Sonnhammer/Chothia tree weights (--wgsc)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
304 <option value="--wblosum">Henikoff simple filter weights (--wblosum)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
305 <option value="--wnone">don't do any relative weighting; set all to 1 (--wnnoe)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
306 <option value="--wgiven">use weights as given in MSA file (--wgiven)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
307 </param>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
308 <when value="--wpb">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
309 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
310 <when value="--wgsc">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
311 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
312 <when value="--wblosum">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
313 <param argument="--wid" type="float" value="0.62" label="Set identity cutoff" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
314 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
315 <when value="--wnone">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
316 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
317 <when value="--wgiven">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
318 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
319 </conditional>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
320 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
321 <token name="@AEEWS@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
322 #if $aeews.aeews_select != "":
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
323 --$aeews.aeews_select
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
324 #if $aeews.aeews_select == "eent":
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
325 --eset $aeews.eset
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
326 --ere $aeews.ere
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
327 --esigma $aeews.esigma
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
328 #elif $aeews.aeews_select == "eclust":
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
329 --eset $aeews.eset
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
330 --eid $aeews.eid
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
331 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
332 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
333 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
334 <xml name="aeews">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
335 <!-- Alternative effective sequence weighting strategies -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
336 <conditional name="aeews">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
337 <param name="aeews_select" type="select" label="Alternative effective sequence weighting strategies">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
338 <option value="">Disabled</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
339 <option value="eent">Adjust eff seq # to achieve relative entropy target (--eent)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
340 <option value="eclust">Eff seq # is the # of single linkage clusters (--eclust)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
341 <option value="enone">No effective seq # weighting: just use nseq (--enone)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
342 </param>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
343 <when value="">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
344 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
345 <when value="eent">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
346 <param argument="--eset" type="float" value="0" label="set eff seq # for all models" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
347 <param argument="--ere" type="float" value="0" label="set minimum rel entropy/position" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
348 <param argument="--esigma" type="float" value="45" label="set sigma param" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
349 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
350 <when value="eclust">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
351 <param argument="--eset" type="float" value="0" label="set eff seq # for all models" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
352 <param argument="--eid" type="float" min="0" max="1" value="0.62" label="set fractional identity cutoff" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
353 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
354 <when value="enone">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
355 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
356 </conditional>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
357 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
358 <token name="@CUT@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
359 $cut_ga
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
360 $cut_nc
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
361 $cut_tc
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
362 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
363 <xml name="cut">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
364 <param argument="--cut_ga" type="boolean" truevalue="--cut_ga" falsevalue="" label="use profile's GA gathering cutoffs to set all thresholding" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
365 <param argument="--cut_nc" type="boolean" truevalue="--cut_nc" falsevalue="" label="use profile's NC gathering cutoffs to set all thresholding" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
366 <param argument="--cut_tc" type="boolean" truevalue="--cut_tc" falsevalue="" label="use profile's TC gathering cutoffs to set all thresholding" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
367 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
368 <token name="@MCSS@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
369 --$mcs.model_construction_strategy_select
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
370
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
371 #if $mcs.model_construction_strategy_select == "fast":
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
372 --symfrac $mcs.symfrac
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
373 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
374 #if str($fragthresh)
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
375 --fragthresh $fragthresh
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
376 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
377 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
378 <xml name="mcss">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
379 <!-- Alternative model construction strategies -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
380 <conditional name="mcs">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
381 <param name="model_construction_strategy_select" type="select" label="Model Construction Strategy">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
382 <option value="fast" selected="true">Assign columns with &gt;= symfrac residues as consensus (--fast)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
383 <option value="hand">Manual construction (requires reference annotation) (--hand)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
384 </param>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
385 <when value="fast">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
386 <param argument="--symfrac" value="0.5" type="float" label="Sets sym fraction controlling --fast construction"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
387 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
388 <when value="hand"></when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
389 </conditional>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
390 <param argument="--fragthresh" type="float" value="0.5" optional="true" label="Fraction of alignment length, under which sequences are excluded" help="HMMER infers fragments if the sequence length L is less than or equal to a fraction x times the alignment length in columns" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
391 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
392 <token name="@PRIOR@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
393 $aps_select
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
394 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
395 <xml name="prior">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
396 <param name="aps_select" type="select" label="Alternative Prior Strategies">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
397 <option value="" selected="true">Unspecified</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
398 <option value="--pnone">Don't use any prior; parameters are frequencies (--pnone)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
399 <option value="--plaplace">Use a Laplace +1 prior (--plaplace)</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
400 </param>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
401 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
402 <xml name="citation">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
403 <citations>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
404 <citation type="doi">10.1093/nar/gkr367</citation>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
405 </citations>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
406 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
407 <token name="@LENGTHS@">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
408 #if str($w_beta):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
409 --w_beta $w_beta
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
410 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
411
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
412 #if str($w_length):
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
413 --w_length $w_length
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
414 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
415 </token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
416 <xml name="lengths">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
417 <param argument="--w_beta" type="float" optional="true" label="Tail mass at which window length is determined" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
418 <param argument="--w_length" type="integer" optional="true" label="Window Length" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
419 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
420 <token name="@INPUTHMMCHOICE@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
421 #if $input_hmm_conditional.input_hmm_source == "history":
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
422 #set $input_hmm_filename = "localref.hmm"
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
423 ln -s '${input_hmm_conditional.hmmfile}' '${input_hmm_filename}' &&
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
424 ## "Press" database
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
425 hmmpress '${input_hmm_filename}' &&
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
426 #else:
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
427 #set $input_hmm_filename = str($input_hmm_conditional.index.fields.db_path)
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
428 #end if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
429 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
430 <xml name="input_hmm_choice">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
431 <conditional name="input_hmm_conditional">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
432 <param name="input_hmm_source" type="select" label="Use a built-in HMM model database or own from your history" >
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
433 <option value="indexed" selected="true">Use a built-in HMM model database</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
434 <option value="history">Use a HMM database from history</option>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
435 </param>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
436 <when value="indexed">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
437 <param name="index" type="select" label="Select a HMM model database" help="If your database of interest is not listed, contact the Galaxy administrator">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
438 <options from_data_table="hmm_database">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
439 <filter type="sort_by" column="2"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
440 <validator type="no_options" message="No indexes are available for the selected input dataset"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
441 </options>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
442 </param>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
443 </when>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
444 <when value="history">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
445 <param name="hmmfile" type="data" format="hmm2,hmm3" label="HMM model" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
446 </when> <!-- history -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
447 </conditional> <!-- input_hmm_conditional -->
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
448 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
449 <xml name="input_hmm">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
450 <param name="hmmfile" type="data" format="hmm2,hmm3" label="HMM model" />
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
451 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
452 <xml name="input_msa">
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
453 <param name="msafile" type="data" label="Multiple Sequence Alignment" format="stockholm,clustal,fasta"
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
454 help="in Stockholm, Clustal, or Fasta format. While this tool accepts fasta, please ensure that the sequences are not unaligned"/>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
455 </xml>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
456
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
457
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
458 <token name="@ACCEL_HEUR_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
459 Acceleration Heuristicts (--F1, --F2, --F3)
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
460 -------------------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
461
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
462 **MSV filter**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
463
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
464 The sequence is aligned to the profile using a specialized model that
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
465 allows multiple high-scoring local ungapped segments to match. The
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
466 optimal alignment score (Viterbi score) is calculated under this multi-
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
467 segment model, hence the term MSV, for “multi-segment Viterbi”. This is
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
468 HMMER’s main speed heuristic. The MSV score is comparable to BLAST’s sum
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
469 score (optimal sum of ungapped alignment segments). Roughly speaking,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
470 MSV is comparable to skipping the heuristic word hit and hit extension
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
471 steps of the BLAST acceleration algorithm.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
472
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
473 The MSV filter is very, very fast. In addition to avoiding indel
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
474 calculations in the dynamic programming table, it uses reduced precision
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
475 scores scaled to 8-bit integers, enabling acceleration via 16-way
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
476 parallel SIMD vector instructions.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
477
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
478 The MSV score is a true log-odds likelihood ratio, so it obeys
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
479 conjectures about the expected score distribution (Eddy, 2008) that
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
480 allow immediate and accurate calculation of the statistical significance
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
481 (P- value) of the MSV bit score.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
482
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
483 By default, comparisons with a P-value of ≤ 0.02 pass this filter,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
484 meaning that about 2% of nonhomol- ogous sequences are expected to pass.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
485 You can use the --F1 option to change this threshold. For example, --F1
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
486 <0.05> would pass 5% of the comparisons, making a search more sensitive
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
487 but slower. Setting the threshold to ≥ 1.0 (--F1 99 for example) assures
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
488 that all comparisons will pass. Shutting off the MSV filter may be
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
489 worthwhile if you want to make sure you don’t miss comparisons that have
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
490 a lot of scattered insertions and deletions. Alternatively, the --max
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
491 option causes the MSV filter step (and all other filter steps) to be
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
492 bypassed.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
493
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
494 The MSV bit score is calculated as a log-odds score using the null model
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
495 for comparison. No correction for a biased composition or repetitive
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
496 sequence is done at this stage. For comparisons involving biased
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
497 sequences and/or profiles, more than 2% of comparisons will pass the MSV
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
498 filter. At the end of search output, there is a line like:
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
499
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
500 Passed MSV filter: 107917 (0.020272); expected 106468.8 (0.02)
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
501
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
502 which tells you how many and what fraction of comparisons passed the MSV
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
503 filter, versus how many (and what fraction) were expected.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
504
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
505 **Viterbi filter**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
506
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
507 The sequence is now aligned to the profile using a fast Viterbi algorithm for
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
508 optimal gapped alignment.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
509
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
510 This Viterbi implementation is specialized for speed. It is implemented in
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
511 8-way parallel SIMD vector instructions, using reduced precision scores that
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
512 have been scaled to 16-bit integers. Only one row of the dynamic programming
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
513 matrix is stored, so the routine only recovers the score, not the optimal
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
514 alignment itself. The reduced representation has limited range; local alignment
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
515 scores will not underflow, but high scoring comparisons can overflow and return
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
516 infinity, in which case they automatically pass the filter.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
517
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
518 The final Viterbi filter bit score is then computed using the appropriate null
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
519 model log likelihood (by default the biased composition filter model score, or
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
520 if the biased filter is off, just the null model score). If the P-value of this
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
521 score passes the Viterbi filter threshold, the sequence passes on to the next
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
522 step of the pipeline.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
523
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
524 The --F2 <x> option controls the P-value threshold for passing the Viterbi
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
525 filter score. The default is 0.001. The --max option bypasses all filters in
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
526 the pipeline. At the end of a search output, you will see a line like:
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
527
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
528 Passed Vit filter: 2207 (0.00443803); expected 497.3 (0.001)
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
529
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
530 which tells you how many and what fraction of comparisons passed the Viterbi
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
531 filter, versus how many were expected.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
532
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
533 **Forward filter/parser**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
534
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
535 The sequence is now aligned to the profile using the full Forward algorithm,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
536 which calculates the likelihood of the target sequence given the profile,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
537 summed over the ensemble of all possible alignments.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
538
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
539 This is a specialized time- and memory-efficient Forward implementation called
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
540 the “Forward parser”. It is implemented in 4-way parallel SIMD vector
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
541 instructions, in full precision (32-bit floating point). It stores just enough
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
542 information that, in combination with the results of the Backward parser
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
543 (below), posterior probabilities of start and stop points of alignments
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
544 (domains) can be calculated in the domain definition step (below), although the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
545 detailed alignments themselves cannot be.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
546
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
547 The Forward filter bit score is calculated by correcting this score using the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
548 appropriate null model log likelihood (by default the biased composition filter
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
549 model score, or if the biased filter is off, just the null model score). If the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
550 P-value of this bit score passes the Forward filter threshold, the sequence
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
551 passes on to the next step of the pipeline.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
552
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
553 The bias filter score has no further effect in the pipeline. It is only used in
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
554 filter stages. It has no effect on final reported bit scores or P-values.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
555 Biased composition compensation for final bit scores is done by a more complex
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
556 domain-specific algorithm, described below.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
557
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
558 The --F3 <x> option controls the P-value threshold for passing the Forward
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
559 filter score. The default is 1e-5. The --max option bypasses all filters in the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
560 pipeline. At the end of a search output, you will see a line like:
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
561
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
562 Passed Fwd filter: 1076 (0.00216371); expected 5.0 (1e-05)
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
563
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
564 which tells you how many and what fraction of comparisons passed the Forward
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
565 filter, versus how many were expected.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
566
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
567 **Bias Filter Options**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
568
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
569 The --max option bypasses all filters in the pipeline, including the bias
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
570 filter.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
571
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
572 The --nobias option turns off (bypasses) the biased composition filter. The
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
573 simple null model is used as a null hypothesis for MSV and in subsequent filter
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
574 steps. The biased composition filter step compromises a small amount of
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
575 sensitivity. Though it is good to have it on by default, you may want to shut
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
576 it off if you know you will have no problem with biased composition hits.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
577
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
578
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
579 **Advanced Documentation**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
580
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
581 A more detailed look at the internals of the various filter pipelines was
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
582 posted on the `developer's blog <http://cryptogenomicon.org/hmmer3-is-stubborn.html>`__.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
583 The information posted there may be useful to those who are struggling with
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
584 poor-scoring sequences.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
585 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
586 <token name="@ADV_OPTS_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
587 Advanced Options
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
588 ----------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
589
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
590 **nonull2**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
591
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
592 can be too aggressive sometimes, causing you to miss homologs. You can turn the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
593 biased-composition score correction off with the --nonull2 option (and if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
594 you’re doing that, you may also want to set --nobias, to turn off another
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
595 biased composition step called the bias filter, which affects which sequences
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
596 get scored at all).
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
597
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
598 **domZ**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
599
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
600 Assert that the total number of targets in your searches is <x>, for the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
601 purposes of per-domain conditional E-value calculations, rather than the number
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
602 of targets that passed the reporting thresholds.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
603
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
604 **Z**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
605
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
606 Assert that the total number of targets in your searches is <x>, for the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
607 purposes of per-sequence E-value calculations, rather than the actual number of
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
608 targets seen.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
609 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
610 <token name="@AEEWS_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
611 Effective Sequence Number
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
612 -------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
613
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
614 After relative weights are determined, they are normalized to sum to a total
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
615 effective sequence number, eff nseq. This number may be the actual number of
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
616 sequences in the alignment, but it is almost always smaller than that. The
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
617 default entropy weighting method (--eent) reduces the effective sequence num-
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
618 ber to reduce the information content (relative entropy, or average expected
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
619 score on true homologs) per consensus position. The target relative entropy is
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
620 controlled by a two-parameter function, where the two parameters are settable
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
621 with --ere and --esigma.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
622
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
623 **--eent**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
624
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
625 Adjust effective sequence number to achieve a specific relative entropy per
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
626 position (see --ere). This is the default.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
627
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
628 **--eclust**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
629
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
630 Set effective sequence number to the number of single-linkage clusters at a
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
631 specific identity threshold (see --eid). This option is not recommended; it’s
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
632 for experiments evaluating how much better --eent is.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
633
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
634 **--enone**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
635
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
636 Turn off effective sequence number determination and just use the actual number
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
637 of sequences. One reason you might want to do this is to try to maximize the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
638 relative entropy/position of your model, which may be useful for short models.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
639
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
640 **--eset**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
641
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
642 Explicitly set the effective sequence number for all models to <x>.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
643
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
644 **--ere**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
645
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
646 Set the minimum relative entropy/position target to <x>. Requires --eent. Default
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
647 depends on the sequence alphabet. For protein sequences, it is 0.59 bits/position;
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
648 for nucleotide sequences, it is 0.45 bits/position.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
649
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
650 **--esigma**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
651
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
652 Sets the minimum relative entropy contributed by an entire model alignment, over
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
653 its whole length. This has the effect of making short models have higher relative
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
654 entropy per position than --ere alone would give. The default is 45.0 bits.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
655
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
656 **--eid**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
657
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
658 Sets the fractional pairwise identity cutoff used by single linkage clustering
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
659 with the --eclust option. The default is 0.62.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
660 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
661 <token name="@ARSWS_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
662 Options Controlling Relative Weights
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
663 ------------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
664
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
665 HMMER uses an ad hoc sequence weighting algorithm to downweight closely related
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
666 sequences and up-weight distantly related ones. This has the effect of making
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
667 models less biased by uneven phylogenetic representation. For example, two
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
668 identical sequences would typically each receive half the weight that one
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
669 sequence would. These options control which algorithm gets used.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
670
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
671
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
672 **--wpb**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
673
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
674 Use the Henikoff position-based sequence weighting scheme [Henikoff and
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
675 Henikoff, J. Mol. Biol. 243:574, 1994]. This is the default.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
676
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
677 **--wgsc**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
678
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
679 Use the Gerstein/Sonnhammer/Chothia weighting algorithm [Gerstein et al, J.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
680 Mol. Biol. 235:1067, 1994].
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
681
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
682 **--wblosum**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
683
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
684 Use the same clustering scheme that was used to weight data in calculating
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
685 BLOSUM subsitution matrices [Henikoff and Henikoff, Proc. Natl. Acad. Sci
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
686 89:10915, 1992]. Sequences are single-linkage clustered at an identity
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
687 threshold (default 0.62; see --wid) and within each cluster of c sequences,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
688 each sequence gets rela- tive weight 1/c.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
689
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
690 **--wnone**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
691
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
692 No relative weights. All sequences are assigned uniform weight.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
693
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
694 **--wid**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
695
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
696 Sets the identity threshold used by single-linkage clustering when using
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
697 --wblosum. Invalid with any other weighting scheme. Default is 0.62.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
698 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
699 <token name="@BIAS_COMP_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
700 Bias Composition
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
701 ----------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
702
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
703 The next number, the bias, is a correction term for biased sequence composition
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
704 that has been applied to the sequence bit score.1 For instance, for the top hit
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
705 MYG PHYCA that scored 222.7 bits, the bias of 3.2 bits means that this sequence
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
706 originally scored 225.9 bits, which was adjusted by the slight 3.2 bit biased-
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
707 composition correction. The only time you really need to pay attention to the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
708 bias value is when it’s large, on the same order of magnitude as the sequence
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
709 bit score. Sometimes (rarely) the bias correction isn’t aggressive enough, and
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
710 allows a non-homolog to retain too much score. Conversely, the bias correction
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
711 can be too aggressive sometimes, causing you to miss homologs. You can turn the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
712 biased-composition score correction off with the --nonull2 option (and if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
713 you’re doing that, you may also want to set --nobias, to turn off another
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
714 biased composition step called the bias filter, which affects which sequences
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
715 get scored at all).
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
716
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
717 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
718 <token name="@CUT_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
719 Options for Model-specific Score Thresholding
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
720 ---------------------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
721
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
722 Curated profile databases may define specific bit score thresholds for each
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
723 profile, superseding any thresholding based on statistical significance alone.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
724 To use these options, the profile must contain the appropriate (GA, TC, and/or
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
725 NC) optional score threshold annotation; this is picked up by hmmbuild from
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
726 Stockholm format alignment files. Each thresholding option has two scores: the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
727 per-sequence threshold <x1> and the per-domain threshold <x2> These act as if
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
728 -T<x1> --incT<x1> --domT<x2> --incdomT<x2> has been applied specifically using
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
729 each model’s curated thresholds.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
730
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
731 **--cut_ga**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
732
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
733 Use the GA (gathering) bit scores in the model to set per-sequence (GA1) and
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
734 per-domain (GA2) reporting and inclusion thresholds. GA thresholds are
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
735 generally considered to be the reliable curated thresholds defining family
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
736 membership; for example, in Pfam, these thresholds define what gets included in
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
737 Pfam Full alignments based on searches with Pfam Seed models.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
738
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
739 **--cut_nc**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
740
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
741 Use the NC (noise cutoff) bit score thresholds in the model to set
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
742 per-sequence (NC1) and per-domain (NC2) reporting and inclusion thresholds. NC
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
743 thresholds are generally considered to be the score of the highest-scoring
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
744 known false positive.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
745
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
746 **--cut_tc**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
747
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
748 Use the NC (trusted cutoff) bit score thresholds in the model to set
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
749 per-sequence (TC1) and per-domain (TC2) reporting and inclusion thresholds. TC
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
750 thresholds are generally considered to be the score of the lowest-scoring known
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
751 true positive that is above all known false positives.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
752 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
753 <token name="@EVAL_CALIB_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
754 Options Controlling H3 Parameter Estimation Methods
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
755 ---------------------------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
756
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
757 H3 uses three short random sequence simulations to estimating the location
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
758 parameters for the expected score distributions for MSV scores, Viterbi scores,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
759 and Forward scores. These options allow these simulations to be modified.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
760
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
761 **--EmL**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
762
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
763 Sets the sequence length in simulation that estimates the location parameter mu
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
764 for MSV E-values. Default is 200.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
765
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
766 **--EmN**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
767
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
768 Sets the number of sequences in simulation that estimates the location parameter
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
769 mu for MSV E-values. Default is 200.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
770
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
771 **--EvL**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
772
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
773 Sets the sequence length in simulation that estimates the location parameter mu
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
774 for Viterbi E-values. Default is 200.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
775
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
776 **--EvN**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
777
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
778 Sets the number of sequences in simulation that estimates the location parameter
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
779 mu for Viterbi E-values. Default is 200.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
780
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
781
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
782 **--EfL**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
783
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
784 Sets the sequence length in simulation that estimates the location parameter tau
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
785 for Forward E-values. Default is 100.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
786
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
787 **--EfN**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
788
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
789 Sets the number of sequences in simulation that estimates the location parameter
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
790 tau for Forward E-values. Default is 200.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
791
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
792 **--Eft**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
793
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
794 Sets the tail mass fraction to fit in the simulation that estimates the location param-
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
795 eter tau for Forward evalues. Default is 0.04.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
796 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
797 <token name="@FORMAT_SELECTOR_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
798 Options for Specifying the Alphabet
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
799 -----------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
800
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
801 The alphabet type (amino, DNA, or RNA) is autodetected by default, by looking
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
802 at the composition of the msafile. Autodetection is normally quite reliable,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
803 but occasionally alphabet type may be ambiguous and autodetection can fail (for
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
804 instance, on tiny toy alignments of just a few residues). To avoid this, or to
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
805 increase robustness in automated analysis pipelines, you may specify the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
806 alphabet type of msafile with these options.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
807 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
808 <token name="@HSSI_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
809 Options Controlling Single Sequence Scoring (first Iteration)
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
810 -------------------------------------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
811
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
812 By default, the first iteration uses a search model constructed from a single
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
813 query sequence. This model is constructed using a standard 20x20 substitution
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
814 matrix for residue probabilities, and two additional pa- rameters for
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
815 position-independent gap open and gap extend probabilities. These options allow
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
816 the default single-sequence scoring parameters to be changed.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
817
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
818 **Gap Open (--popen)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
819
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
820 Set the gap open probability for a single sequence query model to <x>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
821
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
822 **Gap Extend (--pextend)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
823
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
824 Set the gap extend probability for a single sequence query model to <x>.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
825
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
826
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
827 **--mx/--mxfile**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
828
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
829 These options are not currently supported
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
830 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
831 <token name="@LENGTHS_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
832 Tail Mass Options
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
833 -----------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
834
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
835 **Window length tail mass (--w_beta)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
836
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
837 The upper bound, W, on the length at which nhmmer expects to find an instance
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
838 of the model is set such that the fraction of all sequences generated by the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
839 model with length >= W is less than <x>. The default is 1e-7.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
840
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
841
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
842 **Model instance length upper bound (--w length)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
843
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
844 Override the model instance length upper bound, W, which is otherwise
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
845 controlled by --w beta. It should be larger than the model length. The value of
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
846 W is used deep in the acceleration pipeline, and modest changes are not
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
847 expected to impact results (though larger values of W do lead to longer run
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
848 time).
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
849
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
850 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
851 <token name="@MCSS_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
852 **Options Controlling Profile Construction**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
853
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
854 These options control how consensus columns are defined in an alignment.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
855
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
856 **--fast**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
857
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
858 Define consensus columns as those that have a fraction >= symfrac of residues
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
859 as opposed to gaps. (See below for the --symfrac option.) This is the default.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
860
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
861 **--hand**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
862
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
863 Define consensus columns in next profile using reference annotation to the multiple
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
864 alignment. This allows you to define any consensus columns you like.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
865
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
866
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
867 **--symfrac**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
868
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
869 Define the residue fraction threshold necessary to define a consensus column
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
870 when using the --fast option. The default is 0.5. The symbol fraction in each
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
871 column is calculated after taking relative sequence weighting into account, and
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
872 ignoring gap characters corresponding to ends of sequence fragments (as opposed
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
873 to internal insertions/deletions). Setting this to 0.0 means that every
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
874 alignment column will be assigned as consensus, which may be useful in some
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
875 cases. Setting it to 1.0 means that only columns that include 0 gaps (internal
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
876 insertions/deletions) will be assigned as consensus.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
877
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
878 **--fragthresh**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
879
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
880 We only want to count terminal gaps as deletions if the aligned sequence is
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
881 known to be full-length, not if it is a fragment (for instance, because only
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
882 part of it was sequenced). HMMER uses a simple rule to infer fragments: if the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
883 sequence length L is less than or equal to a fraction <x> times the alignment
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
884 length in columns, then the sequence is handled as a fragment. The default is
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
885 0.5. Setting --fragthresh0 will define no (nonempty) sequence as a fragment;
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
886 you might want to do this if you know you’ve got a carefully curated alignment
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
887 of full-length sequences. Setting --fragthresh1 will define all sequences as
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
888 fragments; you might want to do this if you know your alignment is entirely
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
889 composed of fragments, such as translated short reads in metagenomic shotgun
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
890 data.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
891
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
892 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
893 <token name="@OFORMAT_WITH_OPTS_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
894 Options for Controlling Output
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
895 ------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
896
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
897 **Table of hits**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
898
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
899 Save a simple tabular (space-delimited) file summarizing the per-target output, with
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
900 one data line per homologous target model found.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
901
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
902 **Table of per-domain hits**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
903
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
904 Save a simple tabular (space-delimited) file summarizing the per-domain output,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
905 with one data line per homologous domain detected in a query sequence for each
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
906 homologous model.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
907
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
908 **Table of hits and domains in Pfam Format**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
909
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
910 Save an especially succinct tabular (space-delimited) file summarizing the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
911 per-target output, with one data line per homologous target model found.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
912 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
913 <token name="@OFORMAT_WITH_OPTS_NOPFAM_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
914 Options for Controlling Output
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
915 ------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
916
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
917 **Table of hits**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
918
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
919 Save a simple tabular (space-delimited) file summarizing the per-target output, with
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
920 one data line per homologous target model found.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
921
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
922 **Table of per-domain hits**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
923
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
924 Save a simple tabular (space-delimited) file summarizing the per-domain output,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
925 with one data line per homologous domain detected in a query sequence for each
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
926 homologous model.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
927 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
928 <token name="@OFORMAT_WITH_OPTS_N_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
929 Options for Controlling Output
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
930 ------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
931
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
932 **Table of hits**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
933
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
934 Save a simple tabular (space-delimited) file summarizing the per-target output, with
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
935 one data line per homologous target model found.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
936
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
937 **Table of hits (dfam)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
938
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
939 Save a tabular (space-delimited) file summarizing the per-hit output, similar
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
940 to --tblout but more succinct.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
941
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
942
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
943 **List of per-position scores for each hit (--aliscoreout)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
944
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
945 Save to file a list of per-position scores for each hit. This is useful, for
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
946 example, in identifying regions of high score density for use in resolving
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
947 overlapping hits from different models.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
948
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
949 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
950 <token name="@PRIOR_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
951 Options Controlling Priors
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
952 --------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
953
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
954 By default, weighted counts are converted to mean posterior probability
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
955 parameter estimates using mixture Dirichlet priors. Default mixture Dirichlet
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
956 prior parameters for protein models and for nucleic acid (RNA and DNA) models
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
957 are built in. The following options allow you to override the default priors.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
958
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
959 **No priors (--pnone)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
960
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
961 Don’t use any priors. Probability parameters will simply be the observed
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
962 frequencies, after relative sequence weighting.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
963
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
964 **Laplace +1 prior**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
965
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
966 Use a Laplace +1 prior in place of the default mixture Dirichlet prior.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
967 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
968 <token name="@SEED_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
969 Random Seeding
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
970 --------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
971
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
972 Seed the random number generator with <n>, an integer >= 0. If <n> is nonzero,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
973 any stochastic simulations will be reproducible; the same command will give the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
974 same results. If <n> is 0, the random number generator is seeded arbitrarily,
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
975 and stochastic simulations will vary from run to run of the same command.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
976
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
977 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
978 <token name="@THRESHOLDS_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
979 Options for Reporting Thresholds
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
980 --------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
981
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
982 Reporting thresholds control which hits are reported in output files (the main
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
983 output, --tblout, and --domtblout).
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
984
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
985 **E-value (-E)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
986
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
987 In the per-target output, report target profiles with an E-value of <= <x>. The
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
988 default is 10.0, meaning that on average, about 10 false positives will be
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
989 reported per query, so you can see the top of the noise and decide for yourself
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
990 if it’s really noise.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
991
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
992 **Bit score (-T)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
993
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
994 Instead of thresholding per-profile output on E-value, instead report target profiles
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
995 with a bit score of >= <x>.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
996
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
997 **domain E-value (--domE)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
998
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
999 In the per-domain output, for target profiles that have already satisfied the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1000 per-profile reporting threshold, report individual domains with a conditional
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1001 E-value of <= <x>. The default is 10.0. A conditional E-value means the
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1002 expected number of additional false positive domains in the smaller search
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1003 space of those comparisons that already satisfied the per-profile reporting
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1004 threshold (and thus must have at least one homologous domain already).
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1005
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1006 **domain Bit scores (--domT)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1007
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1008 Instead of thresholding per-domain output on E-value, instead report domains
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1009 with a bit score of >= <x>.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1010
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1011 Options for Inclusion Thresholds
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1012 --------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1013
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1014 Inclusion thresholds are stricter than reporting thresholds. Inclusion
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1015 thresholds control which hits are considered to be reliable enough to be
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1016 included in an output alignment or a subsequent search round. In hmmscan, which
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1017 does not have any alignment output (like hmmsearch or phmmer) nor any iterative
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1018 search steps (like jackhmmer), inclusion thresholds have little effect. They
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1019 only affect what domains get marked as significant (!) or questionable (?) in
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1020 domain output.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1021
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1022 **E-value of per target inclusion threshold**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1023
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1024 Use an E-value of <= <x> as the per-target inclusion threshold. The default is
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1025 0.01, meaning that on average, about 1 false positive would be expected in
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1026 every 100 searches with different query sequences.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1027
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1028 **Bit score of per target inclusion threshold**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1029
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1030 Instead of using E-values for setting the inclusion threshold, instead use a
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1031 bit score of >= <x> as the per-target inclusion threshold. It would be unusual
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1032 to use bit score thresholds with hmmscan, because you don’t expect a single
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1033 score threshold to work for different profiles; different profiles have
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1034 slightly different expected score distributions.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1035
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1036 **domain E-value per target inclusion treshold**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1037
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1038 Use a conditional E-value of <= <x> as the per-domain inclusion threshold, in
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1039 targets that have already satisfied the overall per-target inclusion threshold.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1040
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1041 **domain Bit score per target inclusion treshold**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1042
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1043 Instead of using E-values, instead use a bit score of >= <x> as the per-domain
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1044 inclusion threshold. As with --incT above, it would be unusual to use a single
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1045 bit score threshold in hmmscan.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1046
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1047 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1048 <token name="@THRESHOLDS_NODOM_HELP@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1049 Options for Reporting Thresholds
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1050 --------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1051
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1052 Reporting thresholds control which hits are reported in output files (the main
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1053 output, --tblout, and --domtblout).
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1054
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1055 **E-value (-E)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1056
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1057 In the per-target output, report target profiles with an E-value of <= <x>. The
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1058 default is 10.0, meaning that on average, about 10 false positives will be
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1059 reported per query, so you can see the top of the noise and decide for yourself
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1060 if it’s really noise.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1061
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1062 **Bit score (-T)**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1063
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1064 Instead of thresholding per-profile output on E-value, instead report target profiles
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1065 with a bit score of >= <x>.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1066
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1067 Options for Inclusion Thresholds
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1068 --------------------------------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1069
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1070 Inclusion thresholds are stricter than reporting thresholds. Inclusion
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1071 thresholds control which hits are considered to be reliable enough to be
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1072 included in an output alignment or a subsequent search round. In hmmscan, which
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1073 does not have any alignment output (like hmmsearch or phmmer) nor any iterative
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1074 search steps (like jackhmmer), inclusion thresholds have little effect. They
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1075 only affect what domains get marked as significant (!) or questionable (?) in
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1076 domain output.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1077
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1078 **E-value of per target inclusion threshold**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1079
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1080 Use an E-value of <= <x> as the per-target inclusion threshold. The default is
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1081 0.01, meaning that on average, about 1 false positive would be expected in
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1082 every 100 searches with different query sequences.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1083
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1084 **Bit score of per target inclusion threshold**
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1085
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1086 Instead of using E-values for setting the inclusion threshold, instead use a
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1087 bit score of >= <x> as the per-target inclusion threshold. It would be unusual
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1088 to use bit score thresholds with hmmscan, because you don’t expect a single
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1089 score threshold to work for different profiles; different profiles have
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1090 slightly different expected score distributions.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1091
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1092 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1093 <token name="@ATTRIBUTION@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1094
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1095 Attribution
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1096 -----------
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1097
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1098 This Galaxy tool relies on HMMER3_
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1099 Internally the software is cited as:
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1100
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1101 ::
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1102
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1103 # hmmscan :: search sequence(s) against a profile database
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1104 # HMMER 3.1 (February 2013); http://hmmer.org/
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1105 # Copyright (C) 2011 Howard Hughes Medical Institute.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1106 # Freely distributed under the GNU General Public License (GPLv3).
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1107 # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1108
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1109 The wrappers were written by the IUC and are licensed under Apache2_. The
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1110 documentation is copied from the HMMER3 documentation.
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1111
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1112 .. _Apache2: http://www.apache.org/licenses/LICENSE-2.0
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1113 .. _HMMER3: http://hmmer.org/
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1114
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1115
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1116 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1117 <token name="@HELP_PRE@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1118
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1119 What it does
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1120 ============
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
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diff changeset
1121 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1122 <token name="@HELP_PRE_OTH@"><![CDATA[
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1123 Options
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1124 =======
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
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diff changeset
1125 ]]></token>
405dd85a9408 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hmmer3 commit e0d4688a59e6eeba33adcfe803ac43d0bc2863e7"
iuc
parents:
diff changeset
1126 </macros>