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comparison hyphy_relax.xml @ 18:b8bdfac5a326 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 8f76cb8602f79412152a92b267ee016605ae6b8e"
author iuc
date Wed, 23 Dec 2020 20:04:07 +0000
parents ea64cc9a06e4
children 801547975424
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17:ba548f24669a 18:b8bdfac5a326
7 </macros> 7 </macros>
8 <expand macro="requirements"/> 8 <expand macro="requirements"/>
9 <command detect_errors="exit_code"><![CDATA[ 9 <command detect_errors="exit_code"><![CDATA[
10 ln -s '$input_file' relax_input.fa && 10 ln -s '$input_file' relax_input.fa &&
11 ln -s '$input_nhx' relax_input.nhx && 11 ln -s '$input_nhx' relax_input.nhx &&
12
13 export OMP_NUM_THREADS="\${GALAXY_SLOTS:-1}" &&
12 hyphy relax 14 hyphy relax
13 --alignment ./relax_input.fa 15 --alignment ./relax_input.fa
14 --tree ./relax_input.nhx 16 --tree ./relax_input.nhx
15 --models '$analysisType' 17 --models '$analysisType'
18 --code '$gencodeid'
16 #if $treeAnnotations == "2": 19 #if $treeAnnotations == "2":
17 --test TEST 20 --test TEST
18 --reference REFERENCE 21 --reference REFERENCE
19 #else: 22 #else:
20 --test TEST 23 --test TEST
49 ======================================= 52 =======================================
50 53
51 What question does this method answer? 54 What question does this method answer?
52 -------------------------------------- 55 --------------------------------------
53 56
54 Is there ev- idence the strength of selection has been relaxed (or conversely intensified) on a specified group of lineages (TEST) 57 Is there evidence the strength of selection has been relaxed (or conversely intensified) on a specified group of lineages (TEST)
55 relative to a set of reference lineages (RELAX)? Importantly, RELAX is not designed to detect diversifying selection specifically. 58 relative to a set of reference lineages (RELAX)? Importantly, RELAX is not designed to detect diversifying selection specifically.
56 We note that the RELAX framework can perform both this specific hypothesis test as well as fit a suite of descriptive models which address, 59 We note that the RELAX framework can perform both this specific hypothesis test as well as fit a suite of descriptive models which address,
57 or example, overall rate differences between test and reference branches or lineage-specific inferences of selection relaxation. 60 or example, overall rate differences between test and reference branches or lineage-specific inferences of selection relaxation.
58 61
59 Recommended Applications 62 Recommended Applications