Mercurial > repos > iuc > hyphy_absrel

annotate hyphy_absrel.xml @ 36:16093bcfe525 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/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
author iuc
date Tue, 07 Oct 2025 20:43:05 +0000
parents aa96474b3a87
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
35
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
1 <tool id="hyphy_absrel" name="HyPhy-aBSREL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
2 <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
3 <macros>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
4 <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
5 </macros>
33
68916eb8887f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 32
diff changeset
6 <expand macro="bio_tools"/>
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[
24
81e2754865c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents: 17
diff changeset
9 @SYMLINK_FILES@
26
74c8c33c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 24
diff changeset
10 ln -s '$absrel_output' ${input_file}.aBSREL.json &&
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
11 @HYPHYMP@ absrel
24
81e2754865c9 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
iuc
parents: 17
diff changeset
12 --alignment ./$input_file
26
74c8c33c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 24
diff changeset
13 @INPUT_TREE@
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
14 --code '$gencodeid'
26
74c8c33c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 24
diff changeset
15 @branch_options@
3
ba0b2eda907d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 2
diff changeset
16 --output '$absrel_output'
16
f293295d5233 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 7868bb22136a87ff5120042ce90bc6be87d57d80"
iuc
parents: 9
diff changeset
17 --multiple-hits $multiple_hits
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
18 @srv_options@
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
19 --blb $blb
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
20 --kill-zero-lengths $kill_zero_lengths > absrel_stdout.md
26
74c8c33c1b87 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 3908306ffa6f6cbc7b83303b2d4c581406d2fad9"
iuc
parents: 24
diff changeset
21 @ERRORS@
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
22 ]]></command>
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
23 <inputs>
1
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="inputs"/>
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="gencode"/>
0ab5b6856f5d "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"/>
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
27 <section name="advanced_options" title="Advanced Options" expanded="false">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
28 <param argument="--multiple-hits" type="select" label="Include support for multiple nucleotide substitutions" help="Include support for multiple nucleotide substitutions.">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
29 <option value="Double">Include branch-specific rates for double nucleotide substitutions</option>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
30 <option value="Double+Triple">Include branch-specific rates for double and triple nucleotide substitutions</option>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
31 <option value="None" selected="true">Use standard models which permit only single nucleotide changes to occur instantly</option>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
32 </param>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
33 <param argument="--blb" type="float" value="1.0" label="Bag of little bootstrap alignment resampling rate" help="[Advanced option] Bag of Little Bootstraps (BLB) alignment resampling rate (default: 1.0). This parameter controls the fraction of sites to resample for each bootstrap replicate. BLB uses down/upsampling approaches to speed up inference for very long alignments by analyzing subsets of the data."/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
34 <conditional name="srv_conditional">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
35 <param name="srv_enabled" type="select" label="Include synonymous rate variation" help="Include synonymous rate variation.">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
36 <option value="true" selected="true">Yes</option>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
37 <option value="false">No</option>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
38 </param>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
39 <when value="true">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
40 <param argument="--syn-rates" type="integer" value="3" min="1" max="10" label="Synonymous rate classes" help="The number of alpha rate classes to include in the model [1-10, default 3]"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
41 </when>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
42 <when value="false">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
43 </when>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
44 </conditional>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
45 <expand macro="kill_zero_lengths_param"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
46 </section>
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
47 </inputs>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
48 <outputs>
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
49 <data name="absrel_md_report" format="markdown" from_work_dir="absrel_stdout.md" label="aBSREL Report (Markdown) for ${tool.name} on ${on_string}" />
3
ba0b2eda907d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit f14f2bae2b27dc04e574803c7d4442a64cfe43e4"
iuc
parents: 2
diff changeset
50 <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
51 </outputs>
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
52 <tests>
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
53 <test expect_num_outputs="2">
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
54 <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
55 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
35
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
56 <output name="absrel_output">
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
57 <assert_contents>
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
58 <has_text text="fits"/>
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
59 <has_text text="branch attributes"/>
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
60 <has_text text="Full adaptive model"/>
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
61 </assert_contents>
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
62 </output>
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
63 <output name="absrel_md_report">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
64 <assert_contents>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
65 <has_text text="found **1** branches under selection among **5** tested"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
66 </assert_contents>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
67 </output>
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
68 </test>
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
69 <test expect_num_outputs="2">
33
68916eb8887f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 32
diff changeset
70 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
68916eb8887f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 32
diff changeset
71 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
72 <section name="advanced_options">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
73 <param name="multiple_hits" value="Double" />
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
74 </section>
35
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
75 <output name="absrel_output">
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
76 <assert_contents>
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
77 <has_text text="fits"/>
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
78 <has_text text="branch attributes"/>
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
79 <has_text text="Full adaptive model"/>
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
80 </assert_contents>
aa96474b3a87 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
iuc
parents: 33
diff changeset
81 </output>
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
82 <output name="absrel_md_report">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
83 <assert_contents>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
84 <has_text text="found **0** branches under selection among **5** tested"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
85 <has_text text="Branch-level rate at which 2 nucleotides are changed instantly"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
86 </assert_contents>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
87 </output>
33
68916eb8887f "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 4bb2092ac089e709bdc0ec3c3680f47e17be509a"
iuc
parents: 32
diff changeset
88 </test>
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
89 <test expect_num_outputs="2">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
90 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
91 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
92 <section name="advanced_options">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
93 <param name="multiple_hits" value="Double" />
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
94 <conditional name="srv_conditional">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
95 <param name="srv_enabled" value="true" />
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
96 </conditional>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
97 </section>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
98 <output name="absrel_output">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
99 <assert_contents>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
100 <has_text text="fits"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
101 <has_text text="branch attributes"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
102 <has_text text="Full adaptive model"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
103 </assert_contents>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
104 </output>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
105 <output name="absrel_md_report">
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
106 <assert_contents>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
107 <has_text text="found **0** branches under selection among **5** tested"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
108 <has_text text="Branch-level rate at which 2 nucleotides are changed instantly"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
109 <has_text text="The following rate distribution for site-to-site **synonymous** rate variation was inferred"/>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
110 </assert_contents>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
111 </output>
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
112 </test>
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
113 </tests>
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
114 <help><![CDATA[
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
115 aBSREL: Adaptive Branch-Site Random Effects Likelihood
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
116 ======================================================
9
fef84cff2eb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents: 6
diff changeset
117
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
118 **What question does this method answer?**
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
119
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
120 aBSREL (adaptive Branch-Site Random Effects Likelihood) is a powerful method for detecting episodic positive selection. It identifies instances where a proportion of sites along specific branches or lineages of a phylogeny have undergone positive selection.
9
fef84cff2eb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents: 6
diff changeset
121
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
122 **Recommended Applications**
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
123
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
124 1. **Detecting Episodic Diversifying Selection:** Ideal for exploratory testing to find evidence of lineage-specific positive diversifying selection in alignments of various sizes.
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
125 2. **Targeted Branch Testing:** Suitable for targeted testing of branches hypothesized to be under positive selection, even in alignments that would be computationally prohibitive for older branch-site models.
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
126
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
127 **Methodology**
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
128
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
129 aBSREL is an adaptive branch-site random effects likelihood model that allows the dN/dS ratio to vary across sites and branches. The key innovation of aBSREL is its adaptive nature: it infers the optimal number of dN/dS rate classes for each branch, providing a more nuanced and powerful test for positive selection compared to traditional fixed-rate models.
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
130
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
131 **The Intuition**
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
132
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
133 Imagine a gene evolving across a phylogeny. On some branches, the gene might be under strong purifying selection, with most non-synonymous mutations being deleterious. On other branches, the gene might be evolving neutrally. And on a few key branches, the gene might be under positive selection, with non-synonymous mutations providing a fitness advantage.
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
134
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
135 Traditional branch-site models test for positive selection by fitting a model with a fixed number of dN/dS rate classes to each branch. This can be problematic because the evolutionary process is not always so uniform. Some branches might have a simple evolutionary history that can be described by one or two dN/dS rates, while others might have a more complex history that requires more rate classes.
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
136
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
137 aBSREL addresses this by starting with a simple model for each branch and incrementally adding more rate classes until the model fit no longer improves. This "adaptive" approach allows the model to tailor itself to the complexity of the evolutionary process on each branch, leading to a more accurate and powerful test for positive selection.
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
138
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
139 **The Test**
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
140
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
141 For each branch, aBSREL performs a likelihood ratio test to determine if a model that allows for positive selection (i.e., a dN/dS ratio > 1) is a significantly better fit than a model that does not. The p-values from these tests are then corrected for multiple testing to identify branches that show statistically significant evidence of positive selection.
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
142
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
143 **Input**
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
144
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
145 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
146 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
147
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
148 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
149
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
150
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
151 **Output**
2
68d3a06a4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 1
diff changeset
152
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
153 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
154
9
fef84cff2eb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents: 6
diff changeset
155 For each tested branch the analysis will infer the appropriate number of selective regimes,
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
156 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
157
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
158 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
159
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
160 **Further reading**
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
161
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
162 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
163
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
164
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
165 **Tool options**
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
166 ::
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
167
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
168 --alignment [required] An in-frame codon alignment in one of the formats supported by HyPhy
2
68d3a06a4d9b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 533e8f97b4df382944ac8a31d98e04c9efeb6798"
iuc
parents: 1
diff changeset
169
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
170 --tree [conditionally required] A phylogenetic tree (optionally annotated with {})
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
171
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
172 --code Which genetic code to use (see tool form for available options)
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
173
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
174 --branches Which branches should be tested for selection?
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
175 All [default]
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
176 Internal
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
177 Leaves
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
178 Unlabeled branches
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
179 Custom : Enter a branch label
9
fef84cff2eb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents: 6
diff changeset
180
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
181 --multiple-hits Include support for multiple nucleotide substitutions
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
182 Double : Include branch-specific rates for double nucleotide substitutions
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
183 Double+Triple : Include branch-specific rates for double and triple nucleotide substitutions
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
184 None [default] : Use standard models which permit only single nucleotide changes to occur instantly
9
fef84cff2eb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents: 6
diff changeset
185
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
186 --srv Include synonymous rate variation (default: No)
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
187 If Yes, then:
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
188 --syn-rates The number alpha rate classes to include in the model [1-10, default 3]
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
189
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
190 --blb [Advanced option] Bag of Little Bootstraps (BLB) alignment resampling rate (default: 1.0). This parameter controls the fraction of sites to resample for each bootstrap replicate. BLB uses down/upsampling approaches to speed up inference for very long alignments by analyzing subsets of the data. For more details, see https://www.nature.com/articles/s43588-021-00129-5.
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
191
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
192 --output Write the resulting JSON to this file (default is to save to the same path as the alignment file + 'ABSREL.json')
9
fef84cff2eb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents: 6
diff changeset
193
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
194
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
195
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
196 --kill-zero-lengths Automatically delete internal zero-length branches for computational efficiency
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
197 Yes [default] : Automatically delete internal zero-length branches for computational efficiency (will not affect results otherwise)
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
198 Constrain : Keep zero-length branches, but constrain their values to 0
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
199 No : Keep all branches
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
200
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
201 --save-fit Save full adaptive aBSREL model fit to this file (default is not to save)
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
202
9
fef84cff2eb7 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 751182d5067ac8378199058d9152ebfcaeb4c4b5"
iuc
parents: 6
diff changeset
203
6
756a2d3b632b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit ca299e9bbfc25f8e57b5001b8057f2b9e42d0df6"
iuc
parents: 4
diff changeset
204
1
0ab5b6856f5d "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2c7a7ff8a55e7584e84335baa3159a63ce7a590c"
iuc
parents: 0
diff changeset
205 ]]></help>
0
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
206 <expand macro="citations">
36204a7de762 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 538d41e9789e18c8edb3dc68a1aabbee9b9f8bea
iuc
parents:
diff changeset
207 <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
208 </expand>
36
16093bcfe525 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit d97b1b98a3a621c93a7ed9e7db16bda47eefcb92
iuc
parents: 35
diff changeset
209 </tool>