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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
author iuc
date Thu, 02 Mar 2023 15:11:29 +0000
parents fcabcc150d21
children
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6960dd62c983 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hyphy/ commit e7a89841d59689e87db592e112f9c8fb5331d954
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1 <tool id="hyphy_cfel" name="HyPhy-CFEL" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="@PROFILE@">
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2 <description>Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches</description>
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3 <macros>
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4 <import>macros.xml</import>
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5 </macros>
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6 <expand macro="requirements"/>
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7 <command detect_errors="exit_code"><![CDATA[
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8 @SYMLINK_FILES@
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9 hyphy contrast-fel
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10 --code '$gencodeid'
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11 #for $i, $branch in enumerate($branch_repeat):
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12 --branch-set '$branch.branch_label'
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13 #end for
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14 --srv '$srv'
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15 --permutations '$permutations'
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16 --pvalue '$pvalue'
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17 --qvalue '$qvalue'
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18 --output '$cfel_output'
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19 $input_file
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20 @INPUT_TREE@
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21 @ERRORS@
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22 ]]></command>
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23 <inputs>
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24 <expand macro="inputs"/>
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25 <expand macro="gencode"/>
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26 <repeat name="branch_repeat" title="Branch set" min="1">
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27 <param argument="--branch-set" name="branch_label" type="text" value="Test" optional="false" label="Label for set">
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28 <sanitizer invalid_char="">
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29 <valid initial="default" />
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30 </sanitizer>
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31 </param>
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32 </repeat>
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33 <param argument="--permutations" type="boolean" truevalue="Yes" falsevalue="No" label="Perform permutation significance tests"/>
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34 <param argument="--pvalue" type="float" value=".05" min="0" max="1" label="Significance value for site-tests"/>
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35 <param argument="--qvalue" type="float" value=".2" min="0" max="1" label="Significance value for FDR reporting"/>
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36 <param argument="--srv" type="select" label="Include synonymous rate variation" help = "Allow synonymous rates to vary from site to site">
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37 <option value="Yes">Yes (recommended)</option>
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38 <option value="No">No</option>
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39 </param>
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40 </inputs>
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41 <outputs>
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42 <data name="cfel_output" format="hyphy_results.json" />
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43 </outputs>
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44 <tests>
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45 <test>
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46 <param name="input_file" ftype="fasta" value="absrel-in1.fa"/>
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47 <param name="input_nhx" ftype="nhx" value="absrel-in1.nhx"/>
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48 <repeat name="branch_repeat">
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49 <param name="branch_label" value="Internal branches" />
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50 </repeat>
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51 <repeat name="branch_repeat">
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52 <param name="branch_label" value="Terminal branches" />
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53 </repeat>
0
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54 <output name="cfel_output" file="cfel-out1.json" compare="sim_size"/>
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55 </test>
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56 </tests>
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57 <help><![CDATA[
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58 Contrast-FEL : A Test for Differences in Selective Pressures at Individual Sites among Clades and Sets of Branches
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59 ==================================================================================================================
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60
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61 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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62 ]]>
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63
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64 </help>
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65
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66 <expand macro="citations">
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67 <citation type="doi">10.1093/molbev/msaa263</citation>
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68 </expand>
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69 </tool>