Mercurial > repos > iuc > hyphy_busted
annotate hyphy_busted.xml @ 24:e2f03a50aace draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
author | iuc |
---|---|
date | Tue, 20 Apr 2021 10:31:15 +0000 |
parents | c92d5ec5d8d7 |
children | 70fab57f3c05 |
rev | line source |
---|---|
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
1 <?xml version="1.0"?> |
17
c92d5ec5d8d7
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f6cabbd9eb2eea9f5d44fe9836cc5f6d6087a839"
iuc
parents:
10
diff
changeset
|
2 <tool id="hyphy_busted" name="HyPhy-BUSTED" version="@VERSION@+galaxy0" profile="19.09"> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
3 <description>Branch-site Unrestricted Statistical Test for Episodic Diversification</description> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
4 <macros> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
5 <import>macros.xml</import> |
24
e2f03a50aace
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
17
diff
changeset
|
6 <token name="@OPERATION@">BUSTED</token> |
e2f03a50aace
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
17
diff
changeset
|
7 <token name="@operation@">busted</token> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
8 </macros> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
9 <expand macro="requirements"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
10 <command detect_errors="exit_code"><![CDATA[ |
24
e2f03a50aace
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
17
diff
changeset
|
11 @SYMLINK_FILES@ |
3
1d8b63d18f30
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents:
2
diff
changeset
|
12 hyphy busted |
24
e2f03a50aace
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
17
diff
changeset
|
13 --alignment ./$input_file |
e2f03a50aace
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
17
diff
changeset
|
14 #if $input_nhx: |
e2f03a50aace
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
17
diff
changeset
|
15 --tree ./input.nhx |
e2f03a50aace
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
17
diff
changeset
|
16 #end if |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
17 --code $gencodeid |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
18 --branches '$branches' |
3
1d8b63d18f30
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents:
2
diff
changeset
|
19 --output '$busted_output' |
24
e2f03a50aace
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
17
diff
changeset
|
20 > '$busted_log' ; |
e2f03a50aace
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents:
17
diff
changeset
|
21 @CATCH_ERROR@ |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
22 ]]></command> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
23 <inputs> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
24 <expand macro="inputs"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
25 <expand macro="gencode"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
26 <expand macro="branches"/> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
27 </inputs> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
28 <outputs> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
29 <data name="busted_log" format="txt"/> |
3
1d8b63d18f30
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents:
2
diff
changeset
|
30 <data name="busted_output" format="hyphy_results.json" /> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
31 </outputs> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
32 <tests> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
33 <test> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
34 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
35 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> |
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
36 <output name="busted_output" file="busted-out1.json" compare="sim_size"/> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
37 </test> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
38 </tests> |
1
b678fe748dc5
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents:
0
diff
changeset
|
39 <help><![CDATA[ |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
40 |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
41 BUSTED : Bayesian UnresTricted Test of Episodic Diversification |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
42 =============================================================== |
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
43 |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
44 What question does this method answer? |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
45 -------------------------------------- |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
46 |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
47 Is there evidence that some sites in the alignment have been subject to positive diversifying selection, |
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
48 either pervasive (throughout the evolutionary tree) or episodic (only on some lineages)? |
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
49 In other words, BUSTED asks whether a given gene has been subject to positive, diversifying selection at any site, at any time. |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
50 If a priori information about lineages of interest is available (e.g., due to migration, change in the environment, etc.), |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
51 then BUSTED can be restricted to test for selection only on a subset of tree lineages, potentially boosting power. |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
52 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
53 Recommended Applications |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
54 ------------------------ |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
55 |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
56 1. Annotating a collection of alignments with a binary attribute: has this alignment been subject to positive diversifying selection (yes/no)? |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
57 2. Testing small or low-divergence alignments (i.e. ~30 sequences) for evidence of positive diversifying selection, where neither branch nor site level methods have sufficient power. |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
58 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
59 Brief description |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
60 ----------------- |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
61 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
62 BUSTED (branch-site unrestricted statistical test of episodic |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
63 diversification) uses a random effects branch-site model fitted jointly |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
64 to all or a subset of tree branches in order to test for alignment-wide |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
65 evidence of episodic diversifying selection. Assuming there is evidence |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
66 of positive selection (i.e. there is an omega > 1), BUSTED will also |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
67 perform a quick evidence-ratio style analysis to explore which |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
68 individual sites may have been subject to selection. |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
69 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
70 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
71 Input |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
72 ----- |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
73 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
74 1. A *FASTA* sequence alignment. |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
75 2. A phylogenetic tree in the *Newick* format |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
76 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
77 Note: the names of sequences in the alignment must match the names of the sequences in the tree. |
2
f8d88dcef64e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents:
1
diff
changeset
|
78 |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
79 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
80 Output |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
81 ------ |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
82 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
83 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf). |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
84 |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
85 For each tested branch the analysis will infer the appropriate number of selective regimes, |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
86 and whether or not there is statistical evidence of positive selection on that branch. |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
87 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
88 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/BUSTED for an example) |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
89 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
90 Further reading |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
91 --------------- |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
92 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
93 http://hyphy.org/methods/selection-methods/#busted |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
94 |
2
f8d88dcef64e
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents:
1
diff
changeset
|
95 |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
96 Tool options |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
97 ------------ |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
98 :: |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
99 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
100 |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
101 --code Which genetic code to use |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
102 |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
103 --branches Which branches should be tested for selection? |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
104 All [default] : test all branches |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
105 |
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
106 Internal : test only internal branches (suitable for |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
107 intra-host pathogen evolution for example, where terminal branches |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
108 may contain polymorphism data) |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
109 |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
110 Leaves: test only terminal (leaf) branches |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
111 |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
112 Unlabeled: if the Newick string is labeled using the {} notation, |
10
cde38657e82c
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8abccd4b7a288b6a321a6662eec88577ad83b36f"
iuc
parents:
6
diff
changeset
|
113 test only branches without explicit labels |
6
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
114 (see http://hyphy.org/tutorials/phylotree/) |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
115 ]]> |
f9a193154a55
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8d5ae1d04c43988fdcc458f4f08376a15e72db8e"
iuc
parents:
4
diff
changeset
|
116 </help> |
0
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
117 <expand macro="citations"> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
118 <citation type="doi">10.1093/molbev/msv035</citation> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
119 </expand> |
edabb77ac0d4
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff
changeset
|
120 </tool> |