Mercurial > repos > iuc > hyphy_cfel
comparison hyphy_cfel.xml @ 0:3d4ea0544af1 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
| author | iuc |
|---|---|
| date | Tue, 20 Apr 2021 10:26:31 +0000 |
| parents | |
| children | fb833dd994f2 |
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| -1:000000000000 | 0:3d4ea0544af1 |
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| 1 <?xml version="1.0"?> | |
| 2 <tool id="hyphy_cfel" name="HyPhy-CFEL" version="@VERSION@+galaxy0" profile="19.09"> | |
| 3 <description>Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches</description> | |
| 4 <macros> | |
| 5 <import>macros.xml</import> | |
| 6 </macros> | |
| 7 <expand macro="requirements"/> | |
| 8 <command detect_errors="exit_code"><![CDATA[ | |
| 9 ln -s '$input_file' cfel_input.fa && | |
| 10 ln -s '$input_nhx' cfel_input.nhx && | |
| 11 hyphy contrast-fel | |
| 12 --code '$gencodeid' | |
| 13 #for branch in str($branch_set).split(','): | |
| 14 --branch-set '$branch' | |
| 15 #end for | |
| 16 --srv '$srv' | |
| 17 --permutations '$permutations' | |
| 18 --pvalue '$pvalue' | |
| 19 --qvalue '$qvalue' | |
| 20 --output '$cfel_output' | |
| 21 cfel_input.fa | |
| 22 cfel_input.nhx | |
| 23 > '$cfel_log' | |
| 24 @ERRORS@ | |
| 25 ]]></command> | |
| 26 <inputs> | |
| 27 <expand macro="inputs"/> | |
| 28 <expand macro="gencode"/> | |
| 29 <param argument="--branch-set" type="select" multiple="true" min="2" max="2" label="Set of branches to test"> | |
| 30 <option value="Internal branches">Internal branches</option> | |
| 31 <option value="Terminal branches">Terminal branches</option> | |
| 32 <option value="Random set of branches">Random set of branches</option> | |
| 33 <option value="Unlabeled branches">Unlabeled branches</option> | |
| 34 </param> | |
| 35 <param argument="--permutations" type="boolean" truevalue="Yes" falsevalue="No" label="Perform permutation significance tests"/> | |
| 36 <param argument="--pvalue" type="float" value=".05" min="0" max="1" label="Significance value for site-tests"/> | |
| 37 <param argument="--qvalue" type="float" value=".2" min="0" max="1" label="Significance value for FDR reporting"/> | |
| 38 <param argument="--srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site"> | |
| 39 <option value="Yes">Yes (recommended)</option> | |
| 40 <option value="No">No</option> | |
| 41 </param> | |
| 42 </inputs> | |
| 43 <outputs> | |
| 44 <data name="cfel_log" format="txt"/> | |
| 45 <data name="cfel_output" format="hyphy_results.json" /> | |
| 46 </outputs> | |
| 47 <tests> | |
| 48 <test> | |
| 49 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/> | |
| 50 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/> | |
| 51 <param name="branch_set" value="Internal branches,Terminal branches" /> | |
| 52 <output name="cfel_output" file="cfel-out1.json" compare="sim_size"/> | |
| 53 </test> | |
| 54 </tests> | |
| 55 <help><![CDATA[ | |
| 56 Contrast-FEL : A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches | |
| 57 ================================================================================================================== | |
| 58 | |
| 59 A number of evolutionary hypotheses can be tested by comparing selective pressures among sets of branches in a phylogenetic tree. When the question of interest is to identify specific sites within genes that may be evolving differently, a common approach is to perform separate analyses on subsets of sequences and compare parameter estimates in a post hoc fashion. This approach is statistically suboptimal and not always applicable. Here, we develop a simple extension of a popular fixed effects likelihood method in the context of codon-based evolutionary phylogenetic maximum likelihood testing, Contrast-FEL. It is suitable for identifying individual alignment sites where any among the K≥2 sets of branches in a phylogenetic tree have detectably different ω ratios, indicative of different selective regimes. Using extensive simulations, we show that Contrast-FEL delivers good power, exceeding 90% for sufficiently large differences, while maintaining tight control over false positive rates, when the model is correctly specified. We conclude by applying Contrast-FEL to data from five previously published studies spanning a diverse range of organisms and focusing on different evolutionary questions. | |
| 60 ]]> | |
| 61 | |
| 62 </help> | |
| 63 | |
| 64 <expand macro="citations"> | |
| 65 <citation type="doi">10.1093/molbev/msaa263</citation> | |
| 66 </expand> | |
| 67 </tool> |