Mercurial > repos > iuc > hyphy_absrel

annotate hyphy_absrel.xml @ 6:756a2d3b632b draft

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/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
author iuc
date Thu, 20 Feb 2020 22:23:59 +0000
parents 8c79739da199
children fef84cff2eb7
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
36204a7de762 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"?>
4
8c79739da199 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 6b2cd926797bb94fba9d0e319a2dbcff6ee37735"
iuc
parents: 3
diff changeset
2 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@VERSION@+galaxy0">
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
3 <description>adaptive Branch Site Random Effects Likelihood</description>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
4 <macros>
36204a7de762 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>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
6 </macros>
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
7 <expand macro="requirements"/>
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
8 <command detect_errors="exit_code"><![CDATA[
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
9 ln -s '$input_file' absrel_input.fa &&
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
10 ln -s '$input_nhx' absrel_input.nhx &&
3
ba0b2eda907d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 2
diff changeset
11 @HYPHYMPI@ absrel
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
12 --alignment ./absrel_input.fa
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
13 --tree ./absrel_input.nhx
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
14 --code '$gencodeid'
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
15 --branches '$branches'
3
ba0b2eda907d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 2
diff changeset
16 --output '$absrel_output'
ba0b2eda907d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 2
diff changeset
17 #if $log:
ba0b2eda907d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 2
diff changeset
18 > '$absrel_log'
ba0b2eda907d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 2
diff changeset
19 #end if
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
20 ]]></command>
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
21 <inputs>
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
22 <expand macro="inputs"/>
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
23 <param name="log" type="boolean" truevalue="" falsevalue="" label="Output aBSREL log to history"/>
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
24 <expand macro="gencode"/>
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
25 <expand macro="branches"/>
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
26 </inputs>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
27 <outputs>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
28 <data name="absrel_log" format="txt">
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
29 <filter>log</filter>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
30 </data>
3
ba0b2eda907d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 2
diff changeset
31 <data name="absrel_output" format="hyphy_results.json" />
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
32 </outputs>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
33 <tests>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
34 <test>
1
0ab5b6856f5d "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_file" ftype="fasta" value="absrel-in1.fa"/>
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
36 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
37 <param name="log" value="false"/>
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
38 <output name="absrel_output" file="absrel-out1.json" compare="sim_size"/>
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
39 </test>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
40 </tests>
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
41 <help><![CDATA[
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
42
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
43 aBSREL : Adaptive Branch-Site Random Effects Likelihood
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
44 =======================================================
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
45
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
46 What question does this method answer?
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
47 --------------------------------------
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
48
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
49 Is some proportion of sites is subject to positive selection along specific branches or lineages of a phylogeny?
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
50
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
51 Recommended Applications
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
52 ------------------------
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
53
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
54 1. Exploratory testing for evidence of lineage-specific positive diversifying selection in small to medium sized alignments (up to 100 sequences).
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
55 2. Targeted testing of branches selected a priori for positive diversifying selection, including alignments with prohibitive runtimes under older branch-site models (up to 1,000 sequences)
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
56
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
57 Brief description
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
58 -----------------
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
59
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
60 aBSREL (Adaptive branch-site random effects likelihood) uses an adaptive
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
61 random effects branch-site model framework to test whether each branch
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
62 has evolved under positive selection, using a procedure which infers an
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
63 optimal number of rate categories per branch.
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
64
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
65
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
66 Input
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
67 -----
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
68
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
69 1. A *FASTA* sequence alignment.
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
70 2. A phylogenetic tree in the *Newick* format
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
71
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
72 Note: the names of sequences in the alignment must match the names of the sequences in the tree.
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
73
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
74
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
75 Output
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
76 ------
2
68d3a06a4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 1
diff changeset
77
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
78 A JSON file with analysis results (http://hyphy.org/resources/json-fields.pdf).
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
79
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
80 For each tested branch the analysis will infer the appropriate number of selective regimes,
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
81 and whether or not there is statistical evidence of positive selection on that branch.
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
82
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
83 A custom visualization module for viewing these results is available (see http://vision.hyphy.org/aBSREL for an example)
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
84
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
85 Further reading
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
86 ---------------
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
87
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
88 http://hyphy.org/methods/selection-methods/#absrel
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
89
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
90
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
91 Tool options
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
92 ------------
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
93 ::
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
94
2
68d3a06a4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 1
diff changeset
95
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
96 --code Which genetic code to use
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
97
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
98 --branches Which branches should be tested for selection?
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
99 All [default] : test all branches
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
100
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
101 Internal : test only internal branches (suitable for
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
102 intra-host pathogen evolution for example, where terminal branches
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
103 may contain polymorphism data)
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
104
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
105 Leaves: test only terminal (leaf) branches
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
106
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
107 Unlabeled: if the Newick string is labeled using the {} notation,
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
108 test only branches without explicit labels
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
109 (see http://hyphy.org/tutorials/phylotree/)
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
110
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
111
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
112
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
113 ]]></help>
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
114 <expand macro="citations">
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
115 <citation type="doi">10.1093/molbev/msv022</citation>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
116 </expand>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
117 </tool>