Mercurial > repos > iuc > hyphy_cfel

annotate hyphy_cfel.xml @ 0:3d4ea0544af1 draft

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"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
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children fb833dd994f2
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3d4ea0544af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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1 <?xml version="1.0"?>
3d4ea0544af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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2 <tool id="hyphy_cfel" name="HyPhy-CFEL" version="@VERSION@+galaxy0" profile="19.09">
3d4ea0544af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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3 <description>Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches</description>
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4 <macros>
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5 <import>macros.xml</import>
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6 </macros>
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7 <expand macro="requirements"/>
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8 <command detect_errors="exit_code"><![CDATA[
3d4ea0544af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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9 ln -s '$input_file' cfel_input.fa &&
3d4ea0544af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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10 ln -s '$input_nhx' cfel_input.nhx &&
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11 hyphy contrast-fel
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12 --code '$gencodeid'
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13 #for branch in str($branch_set).split(','):
3d4ea0544af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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14 --branch-set '$branch'
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15 #end for
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16 --srv '$srv'
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17 --permutations '$permutations'
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18 --pvalue '$pvalue'
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19 --qvalue '$qvalue'
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20 --output '$cfel_output'
3d4ea0544af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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21 cfel_input.fa
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22 cfel_input.nhx
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23 > '$cfel_log'
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24 @ERRORS@
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25 ]]></command>
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26 <inputs>
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27 <expand macro="inputs"/>
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28 <expand macro="gencode"/>
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29 <param argument="--branch-set" type="select" multiple="true" min="2" max="2" label="Set of branches to test">
3d4ea0544af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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30 <option value="Internal branches">Internal branches</option>
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31 <option value="Terminal branches">Terminal branches</option>
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32 <option value="Random set of branches">Random set of branches</option>
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33 <option value="Unlabeled branches">Unlabeled branches</option>
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34 </param>
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35 <param argument="--permutations" type="boolean" truevalue="Yes" falsevalue="No" label="Perform permutation significance tests"/>
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36 <param argument="--pvalue" type="float" value=".05" min="0" max="1" label="Significance value for site-tests"/>
3d4ea0544af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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37 <param argument="--qvalue" type="float" value=".2" min="0" max="1" label="Significance value for FDR reporting"/>
3d4ea0544af1 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit 2742ee3b4e90f65352845265d2f85c4263e0eabb"
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38 <param argument="--srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site">
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39 <option value="Yes">Yes (recommended)</option>
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40 <option value="No">No</option>
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41 </param>
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42 </inputs>
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43 <outputs>
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44 <data name="cfel_log" format="txt"/>
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45 <data name="cfel_output" format="hyphy_results.json" />
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46 </outputs>
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47 <tests>
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48 <test>
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49 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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50 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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51 <param name="branch_set" value="Internal branches,Terminal branches" />
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52 <output name="cfel_output" file="cfel-out1.json" compare="sim_size"/>
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53 </test>
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54 </tests>
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55 <help><![CDATA[
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56 Contrast-FEL : A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches
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57 ==================================================================================================================
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58
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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.
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60 ]]>
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61
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62 </help>
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63
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64 <expand macro="citations">
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65 <citation type="doi">10.1093/molbev/msaa263</citation>
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66 </expand>
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67 </tool>